We applied several benchmarking methods to evaluate the sensitivity of our method to detect mutations as a function of sequencing depth and allelic fraction (Fig. 2b). First, we calculated the sensitivity under a model of independent sequencing errors and accurate read placement using our statistical test given an allelic fraction, tumor sequencing depth and assuming all bases have a fixed base quality score of Q35 (approximate mean base quality score in simulation data; Online Methods; Supplementary Fig. 4).
