In their paper on exome techniques the authors have also compared SNVs detected with exome sequencing with those detected from a whole genome sequencing on the same sample. Results are quite interesting! They found that, considering the coding regions, a significant proportion of the identified variants (few thounsands) are different comparing WGS and WES data. In most cases this is explained by the fact that WGS cover some exon regions that capture kits simply miss meanwhile WES have a deeper coverage and so allows detection of variants in some regions which are low-covered with the whole genome sequencing. However a few hundred of variants remain that are uniquely identified by one of the two techniques...and this is quite away from expected...since one usually think that a WGS approach with adequate coverage will identify all the variants from a WES (plus of course many others located in the non-coding regions). Moreover about 300 SNVs that were identified by all three of the exome sequencing platforms but not by WGS are associated with human diseases, suggesting that exome sequencing can pick up variants with clinical relevance that WGS alone would miss.
"It was definitely surprising to me that the exome [sequencing] was finding information that the genome [sequencing] did not pick up," said Snyder. "Some of these are important regions — you can't just blow these off.". Given these results, it might make sense to do both WGS and exome sequencing "to make sure you are really covering your exome variants," he said. "If you can afford it, that's a good thing to do since you will get extra information from your exome that you would not have gotten from the genome."I post also an image from the original article that help visualizing this idea!