CopywriteR compares to dedicated copy number detection methods. (A) Six PDX-derived human melanoma were subjected to WES and analyzed on SNP6 arrays. Pseudo counts were derived (see Materials and methods), and used as a basis for copy number profiles, with segmentation values (CBS) depicted in red (left panel). After segmentation, segmentation values were represented as a heatmap to show concordance of the two methods. (B) Four murine small-cell lung carcinomas (SCLC) were subjected to WES and analyzed by arrayCGH. Pseudo counts were created and used for creating copy number profiles, with segmentation values (CBS) depicted in red (right panel). Segmentation values were plotted as in (A) for comparison of the two methods (left panel). (C) Tumor T20 from a breast cancer mouse model was subjected to WES or LC-WGS. Copy number profiles of chromosome 12 generated with onTarget or CopywriteR methods are compared to the profile from LC-WGS data of the same material, with segmentation values (CBS) depicted in red (left panel). Segmentation values of onTarget and CopywriteR methods are plotted against the LC-WGS method, and Euclidian distances and Pearson correlation coefficients of segmentation values are displayed (right panel).