Fig. 3

CNV and b-allele frequency scatter plot as provided by CNVizard for chromosome 1. A somatic loss of heterozygosity is visible, indicated by the dispersion of the grey dots towards 1 and 0 in the B-allele frequency plot (B) on the left side (p arm) compared to the normal bi-allelic state on the right side of the plot (q arm). The CNV plot shows three small CNVkit-called copy number alterations (red dots in the CNV plot (A)). Grey dots indicate the copy number of a single bin as analyzed by CNVkit [4]. Regions with copy number changes called by CNVkit, are indicated by red dots. The x-axis depicts the chromosomal position in Mb and the y-axis, either the log2 copy number or the allele frequency ratio. Plots are generated using matplotlib [12] and seaborn [13]. The user can modify the displayed region (either the whole genome or a single chromosome) and the color of dots for copy number changes