Finally, each variant detected in the tumor is designated as somatic (not present in the matched normal), germline (present in the matched normal) or variant (present in the tumor, but indeterminate status in the matched normal due to insufficient data). To perform this classification, we use a LOD score that compares the likelihood of the data under models in which the variant is present as a heterozygote or absent in the matched normal (Online Methods). We declare that there are insufficient data for classification if the power to make a germline classification is less than 95%. We also make use of public germline variation databases41 as a prior probability of an event being germline.
