Targeted deep sequencing of specific genes or regions is of great interest in clinical cancer diagnostics where some sequence variants, particularly translocations and indels, have known prognostic or diagnostic significance. In this setting, it is unnecessary to sequence an entire genome, and target capture methods can be applied to limit sequencing to important regions, thereby reducing costs and the time required to complete testing. Existing next-gen sequencing analysis packages are optimized for efficiency in whole-genome studies and are unable to benefit from the particular structure of targeted sequence data.