Genomic information from the patient is becoming increasingly important for diagnosis of many diseases. Next Generation Sequencing (NGS), while commonly used as a research tool, is steadily making its way into clinical labs. One advantage of NGS is found in the observations that can be made, in addition to primary sequence, by analyzing raw data. This project is focused on the development of three such applications that have diagnostic utility. The first is a method to determine the phase of compound heterozygotes; an important problem when recessive genes contain more than one mutation. The second is a process designed to identify and interpret chromosomal rearrangements that are related to disease. And finally, the third is a technique used to calculate the copy number of mitochondrial DNA. These methods were developed for use in the clinical lab and can have a practical role in diagnosing disease.