Estimating the copy number at a locus of interest

It is often of interest to know how often a sequence occurs in a sample of interest—that is, to estimate whether, in your particular sample, a locus has been duplicated or its copy number has increased. The locus could be anything from a gene at Kbp scale or a large section of DNA at Mbp scale. Our approach in this recipe will be to use HTS read coverage after alignment to estimate a background level of coverage and then inspect the coverage of our region of interest. The ratio of the coverage in our region of interest to the background level will give us an estimate of the copy number in the region. The recipe here is the first step. The background model we use is very simple—we calculate only a global mean, but we'll discuss some alternatives later. Also, this recipe does not cover ploidy—the number...