Figure S23 shows the true positive rate (TPR) against the false discovery rate (FDR) for 2422 realistic (3131 ideal) simulated crossover events from 1830 (2120 ideal) informative meioses. In the simulations with realistic levels of genotyping error (Figure S23 top left), Merlin detects 90.57% of events but with a substantial FDR of 62.48% while SHAPEIT2 has a FDR of 2.89% at the same rate of detection. SHAPEIT2 has the additional advantage of having a probability associated with each event, which can be thresholded. For example, by setting a threshold of we can achieve a FDR = 3.78% and TPR = 92.4% or for FDR = 0.58% and TPR = 69.45%. In the absence of genotyping error (Figure S23 bottom left) the performance of Merlin is improved (FDR = 3.48% and TPR = 95.66%) but SHAPEIT2 is marginally better (FDR = 0.71% and TPR = 95.75% at ).
