Tools for genotyping copy number in whole-genome sequencing (WGS) data exist. Despite their availability, there are a limited number of tools that efficiently process this data at scale with rapid compute time, low memory usage, and easy to parse outputs. This is critical as WGS continues to be housed in the “cloud.” Copy Number Private Investigator (CNPI) is a computational toolkit (https://github.com/TNTurnerLab/CNPI) that performs several tasks including genotyping of regions of interest, digital karyotype determination, assessment of chromosomal sex, plotting of copy number in regions of the genome, and generation of an Individual-level Copy Number Score (ICNS). Inputs to CNPI include copy number estimates, genome-wide, from WGS data and a corresponding reference annotation file. With these inputs, CNPI can genotype any regions of the genome rapidly. For example, all genes in the genome can be genotyped in