Performance of PennCNV and MinimumDistance on simulated data. Each point represents a synthetic 25,000 basepair chromosome in which the number of markers incorrectly called de novo (a) or not de novo (b) were tabulated for PennCNV and MinimumDistance. Log R ratios were simulated with three different levels of correlation between individuals in the trio (columns) and four different levels of variance (rows). The diagonal line in each panel is the identity. (a) False positive frequencies in PennCNV and MinimumDistance are uncorrelated, with more skewed frequencies in PennCNV that were threshold at 80 to fit on the display. The mean false positive frequency in MinimumDistance is lower than PennCNV over a range of variance and correlation settings (large circles). The gray horizontal and vertical dashed lines correspond to false positive rates of 0.001. (b) The number of markers falsely called de novo is highly correlated between methods. The mean false negative frequency is comparable in PennCNV and MinimumDistance (large circles). The gray horizontal and vertical dashed lines denote false negative rates of 0.1.
Scharpf et al. BMC Bioinformatics 2012 13:330 doi:10.1186/1471-2105-13-330