I have whole exome sequencing data from insect individuals from two different populations. I'm interested to see if there are any genome regions that have much better coverage in one population than in the other. (For example, I want to see if the exome capture probes work much better for one population, or see if there are any large deletions.) Would there be any problem, conceptually, with using edgeR for this purpose? They're both dealing with read abundances that vary between individuals and groups of samples. In principle, is calculating differential coverage and calculating its statistical significance different from doing the same thing for differential gene expression?