Copy number detection in the absence of a reference. (A) CopywriteR and onTarget methods were applied to WES data of melanoma PDX sample T99, either with or without C43 as a reference. Genome-wide copy number profiles are shown, with segmentation values (CBS) depicted in red. (B) CBS-derived segmentation values of the analysis in (A) are represented in a heatmap. (C) Segmentation values of all six melanoma PDX samples were treated as in (A) and (B), and the weighted Euclidian distances and Pearson correlation coefficients were calculated for every sample between the different methods. The means of those values across all samples are represented as clustered heatmaps.