To measure the false positive rate due to tumor over-calling, we used the virtual tumor approach across 1 Gb of NA12878 at various depths in the virtual tumor and at 30x in the virtual normal. All detected events are false positives, but to eliminate those due to under-calling germline events from consideration, we excluded all known germline variant sites. Using no filters (STD) the false positive rate increased with depth (from 6.7/mb at 5x to 20.1/mb at 30x) (Fig. 3a). This is due to the increased power to call mutations with lower allele fractions, which are enriched with false positives (Fig. 3b). The HC filters reduce the false positive rate by an order of magnitude (1.00/mb at 30x). The Panel of Normals (HC+PON) then filters out remaining rare, but recurrent, artifacts (0.51/mb at 30x). Certain filters, such as the Poor Mapping filter, have the biggest effect at low depths whereas other filters are more invariant to depth, such as the Proximal Gap filter (Fig. 3c). The Clustered Position filter rejects the most sites exclusively. However, the majority of false positives are rejected by several filters.
