Fig. 2

Performance comparison of variant callers with default parameters. a Sensitivity of variant callers as a function of the variant allele frequency. To make the predictions comparable we selected the largest set of variants from the top of the list of each caller such that the false discovery rate is still below α. We show plots for α equal to 0.05 (solid lines), and 0.1 (dashed lines). If the tool has a very good precision, the two curves for the two α cutoffs are identical, as it is the case for MuTect and VarScan2. The details on how the sensitivities are displayed can be found in Additional file 1: Section G. b Area under precision recall curve as a function of the coverage. Again the two cutoffs for the false discovery rate α=0.05, and α=0.1 are chosen (see Additional file 1: Section C). The coverages correspond to the five different levels (12, 25, 50, 75, and 100%) displayed in Fig. 1 in step 5