Fig. 2

Simulation results for the integrated breakpoint model and an equivalent hidden Markov model (HMM) with postprocessing to infer breakpoint copy number. Also shown are results for the breakpoint model with perfect initialization. Two sets of simulations were performed, varying fraction of the descendant tumour clone (left column) and proportion of the genome with divergent copy number (right column). Boxplots show proportion of the genome (a, b) and proportion of breakpoints (c, d) for which the tool correctly called clone-specific copy number, in addition to relative normal fraction error (e, f) and relative minor clone fraction error (g, h). Boxes show the interquartile (IQR) range with a line depicting the median. Whiskers extend 1.5×IQR above quartile 3 and below quartile 1. Diamonds show positions of outlier data points