Probe-level copy ratio (.cnr) and segmentation (.seg) files for 137 keratinocyte samples

Copy number was inferred from individual keratinocytes using CNVkit, a Python library and command-line software toolkit to infer and visualize copy number from either DNA-sequencing or RNA-sequencing data. CNVkit produces .<i>cnr</i> files (probe-level copy ratio files) which feature bin-level log2 ratios. These files contain columns for chromosome or reference sequence name, start and end positions, gene name, log2 mean coverage depth, and each bin’s proportional weight or reliability. CNVkit also generates <i>.cns</i> files (segmentation files) which feature segmented log2 ratios. These files share similar columns to <i>.cnr</i> files but with rows corresponding to segments rather than individual probes. It also includes an additional "probe" column, indicating the number of bins covered by the segment. Exporting the segmentation files of multiple samples result in a <i>.seg</i><i> </i>file, which can be loaded in the Integrative Genomic Viewer (IGV).The documentation for CNVKit can be found in Talevich, E., Shain, A. H., <i>et al.,</i> "CNVkit: Genome-Wide Copy Number Detection and Visualization from Targeted DNA Sequencing" and Talevich, E., Shain, A. H., "CNVkit-RNA: Copy number inference from RNA-Sequencing data." It can also be accessed here https://github.com/etal/cnvkit.In this extended dataset, we have provided a zipped folder containing 137 <i>.cnr</i> files and a <i>.seg</i> file for all keratinocyte samples genotyped in this study.