Estimating the copy number at a locus of interest

We will often want to know how often a sequence occurs in a sample of interest – that is, to estimate whether in a given sample, a locus has been duplicated or its copy number has increased. The locus could be anything from a gene at a Kbp scale or a large section of DNA at a 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 compare it to the coverage in a region of interest. The ratio will give us an estimate of the copy number of our region of interest. The recipe here is the first step. The background model we’ll use is very simple – we’ll only calculate a global mean, but we’ll discuss some alternatives later. This recipe does not cover ploidy – the number of genomes present in the whole cell. It is possible to estimate ploidy from similar data but it is a more involved pipeline. Take a look at the...