Fig. 3
From: PureCN: copy number calling and SNV classification using targeted short read sequencing
B-allele plot of the male breast cancer metastasis example. In all 3 panels, a dot represents a germline SNP (in single sample mode a predicted germline SNP). The first panel (a) shows their allelic fractions along the genome. Background colors visualize chromosomes and vertical dotted lines centromere positions. The bold black lines visualize the expected (not the average) allelic fractions in the segment. These expected values are calculated using the estimated purity and the total (sum of maternal and paternal copy number) and minor (the minimum of maternal and paternal copy number) segment copy numbers (Eq. 5). These are visualized in black and grey, respectively, in the (b) and (c). Panel (b) shows the copy number log-ratios, panel (c) the final, inferred integer copy numbers. SNPs plotted as triangles or crosses were classified as potential homozygous or contamination, respectively