1. A computer implemented method of differentially filtering genetic data, which comprises: accessing, by a computer comprising a processor and a memory, data of intensity measurements corresponding to hybridization of target nucleic acids to an array of single nucleotide polymorphism nucleic acid probes and copy number nucleic acid probes, wherein the single nucleotide polymorphism nucleic acid probes are designed to identify one or more single nucleotide polymorphisms in the target nucleic acids and the copy number nucleic acid probes are designed to identify one or more copy number variations in the target nucleic acids; applying, by the processor, one or more algorithms stored in memory to the data of the intensity measurements to analyze and convert the data of the intensity measurements to genetic data selectable by a user on at least one input interface window; displaying the genetic data on a visual display device connected to the computer, wherein the computer comprises a computer program configured to visually display the genetic data to a user on the visual display device in a display area comprising a plurality of user configurable windows displayed on the visual display device, wherein the plurality of user configurable windows comprises a multiple chromosomes view, a selected chromosome view, and a segment filters view, wherein each view comprises at least one genomic map obtained from the genetic data; presenting the user with an input interface via the computer, wherein the input interface is presented on the visual display device and receives input from the user via an interface including the at least one genomic map to modify the views of the user configurable windows; receiving, by the computer and from the input interface, a selection of a subset of genetic data designated as one or more regions of genetic data characterized by loss of heterozygosity, long continuous stretches of homozygosity, copy number mosaicism, or copy number variation; receiving, by the computer and from the user through the at least one input interface window, a first set of parameters selected by the user for filtering the one or more regions of genetic data; differentially filtering, by a processor of the computer, the subset of genetic data in response to receiving the first set of parameters by determining a first filtered subset of the genetic data that corresponds to the first set of parameters; and displaying on the visual display device, the first filtered subset of the genetic data corresponding to the first set of parameters nearly simultaneously as the first set of parameters is received by the computer, wherein the first filtered subset of genetic data is visualized using various colors, icons or other visual markers in the user configurable windows to distinguish from the genetic data that does not correspond to the first set of parameters.