Figure 5.

Comparison of specificity for detecting simulated allelic imbalances for different methods. Heterozygous SNPs in NA06991 were used to estimate the specificity of methods for detecting allelic imbalances with increasing normal cell contamination in the simulated data set. (a) Specificity for calls of allelic imbalance or not in the simulated data set. Lines correspond to specificity for PennCNV (black), QuantiSNP (green), unpaired segmentation (red), paired segmentation (orange), and SOMATICs (blue). (b) Size and number of erroneously called regions for PennCNV (black), QuantiSNP (green), unpaired segmentation (red), paired segmentation (orange), and SOMATICs (blue) across the entire simulated data set. Segment size is in consecutive erroneously called heterozygous SNPs. Only regions larger than four heterozygous SNPs are shown. (c) Specificity for correct calling of the type of allelic imbalance in the simulated data set. Lines correspond to specificity for PennCNV (black), QuantiSNP (green), unpaired segmentation (red), paired segmentation (orange), and SOMATICs (blue).