Whole genome sequence (WGS) is often used in CNV discovery. However, until sequencing costs drop dramatically, it is simply not feasible to generate the high coverage (> 10x) whole genome sequence, suggested for CNV detection, on large numbers of animals. Due to its cost-effectiveness, WES is routinely used for the detection of coding sequence variation (Guo et al., 2013). In humans, the exome comprises approximately 1–3% of the genome, but accounts for over 85% of all mutations identified in Mendelian disorders (Ng et al., 2010), making it a desirable and practical approach for investigating variations in coding sequence.