There are several major algorithms that are used to find large deletions (structural variants, or SVs). Most of them rely on a pair of sequencing reads spanning the breakpoints of the SV. If you have WGS data, the chance that you sequenced across the breakpoint is pretty good, but for WES data, it's much less likely that the breakpoint is in the sequenced region. So, you want to focus on SV calling tools that use read count (also referred to as read depth or coverage), and don't require spanning reads. Some read count-based tools that can handle WES data include EXCAVATOR, CoNIFER, and ExomeCNV. I would recommend using at least two different tools, as there tends to be a lot of noise when calling SVs, and looking at concordance between callers is one way to find the true signal.