Based on this analysis, we observe that MuTect is a highly sensitive detection method. It detects mutations at a site with 30x depth in the tumor (typical of whole genome sequencing) and an allele fraction of 0.2 with 95.6% sensitivity. The sensitivity can be increased to 99.9% by sequencing deeper (to 50x), and drops to 58.9% for detecting mutations with allelic fraction of 0.1 (at 30x) (Fig. 2b, Supplementary Table 1). Furthermore, with 150x depth (typical of exome sequencing) we have 66.4% sensitivity for 3% allele fraction events. It is this sensitivity to detect low-allele fraction events that uniquely positions MuTect to analyze samples with low purity or with complex subclonal structure.
