Systems and methods for storing large data sets, such as genetic sequence information. Within a “targeted subset” of positions with information, the system stores, both variant states and missing states at each position. Reference states are not stored, but are inferred within the targeted subset when neither a variant nor a missing state is stored at a given position. The absence of a variant state at a given position is assumed to be a reference state. The criteria for missing data are defined in pre-processing and are customizable based on the use case. For example, each data point may represent the genetic information of a sample at a position in the genome. The targeted subset may represent those positions that were included in a sequencing test.