Please excuse me for I know the question is quite vague and doesn't actually explain what I have in mind. Here is my question. I sequenced human exomes for clinical purposes, so my goal is to determine if there is a variant in one of my genes of interest that explains the disease in question. The technical issue here is that how well did we capture/sequence the genes (exones) in question. I can get the coverage data but I would like to get your input in interpreting the data. Now very low coverage is not good since the whole idea is to benefit from redundancy in the next gen sequencing data and more (good quality mapped reads to this region is beter) but also when you have a lot of reads (i.e >150X) there can be something funny going on here as well such as a repeat region or a low complexity region that allows reads from different sites to map to this part of the genome. In short what would be a good heuristics/algorithm to decide if the next gen exome/genome sequencing reaction was good enough to move forward with further analysis to confidently make decisions for genetic causes of a disease?