Fig. 2
Comparison of sensitivity and specificity of MuSE and MuTect using synthetic data. a Comparison of sensitivity and specificity of MuSE (solid line), MuTect (dotted line), SomaticSniper (solid square), and Strelka (solid triangle) using the synthetic data IS1, IS2, and IS3 from the ICGC-TCGA DREAM Mutation Calling challenge. The numbers of positions with positive conditions are 3535, 4322, and 7903, respectively. Both tumor and matched-normal data have ∼ 30× average coverage. The three synthetic data sets are color-coded using red, blue, and orange, respectively, and the associated ROC curves, focusing on an FPR between 0 and 1×10−6, are ordered from top left to bottom right. The tier-based sample-specific cutoffs of MuSE and the MuTect default cutoff are labeled correspondingly. The embedded plot focuses on a narrow range of true positive rates. The two times when PASS cutoffs were identified are listed at the bottom right corner. Sensitivity and specificity of VarScan2 (not plotted because they were out of bounds) were 0.9859 and 8.369×10−6 (IS1), 0.9704 and 1.294×10−6 (IS2), and 0.8602 and 1.478×10−6 (IS3), respectively. b Comparison of sensitivity and specificity of MuSE (blue line) and MuTect (red line) using the virtual-tumor benchmarking approach. The ROC curves focus on an FPR between 0 and 5×10−6. Tumor sample sequencing depth varies from 10× to 60×, and matched-normal sample sequencing depth is fixed at 30×. Four scenarios of spike-in VAF 0.05 (dot-dashed), 0.1 (dotted), 0.2 (dashed), and 0.4 (solid) are plotted for every sequencing depth. The tier-based sample-specific cutoffs of MuSE and the MuTect default cutoff are labeled accordingly. Some MuSE cutoffs are close to each other and overlap on the plot. For 30× coverage, the two times that Tier 1 cutoffs were identified are listed at the bottom right corner of the corresponding subplot