A computer-implemented method of identifying at least one structural variation in a population of genomes from individuals, the method comprising: assembling single nucleotide polymorphism data from parents and their offspring; analyzing the SNP data using a software program for at least one non-Mendelian inheritance pattern, wherein the NMI is a potential structural variation; characterized in that the method further comprises: scoring the NMI to identify large structural variations from sequential SNPs that demonstrate NMI in the offspring; removing SNPs that demonstrate NMI in the offspring but that overlap with known existing variation; identifying conserved regions of the genome, using a custom correlation coefficient analysis, to filter regions that should be conserved based on the CCC analysis but include a structural variation; and screening for potentially biologically important structural variation, the potentially biologically important structural variation is selected from one or more of a structural variation that resides in a gene in which less than 5% of normal individuals have a known structural variation; there is a custom correlation coefficient bloc in the gene; a frequency of the NMI at one site in the gene is greater than 5% in a diseased population; and there is a run of at least four SNPs with NMI in a row. assembling single nucleotide polymorphism data from parents and their offspring; analyzing the SNP data using a software program for at least one non-Mendelian inheritance pattern, wherein the NMI is a potential structural variation; characterized in that the method further comprises: scoring the NMI to identify large structural variations from sequential SNPs that demonstrate NMI in the offspring; removing SNPs that demonstrate NMI in the offspring but that overlap with known existing variation; identifying conserved regions of the genome, using a custom correlation coefficient analysis, to filter regions that should be conserved based on the CCC analysis but include a structural variation; and screening for potentially biologically important structural variation, the potentially biologically important structural variation is selected from one or more of a structural variation that resides in a gene in which less than 5% of normal individuals have a known structural variation; there is a custom correlation coefficient bloc in the gene; a frequency of the NMI at one site in the gene is greater than 5% in a diseased population; and there is a run of at least four SNPs with NMI in a row. scoring the NMI to identify large structural variations from sequential SNPs that demonstrate NMI in the offspring; removing SNPs that demonstrate NMI in the offspring but that overlap with known existing variation; identifying conserved regions of the genome, using a custom correlation coefficient analysis, to filter regions that should be conserved based on the CCC analysis but include a structural variation; and screening for potentially biologically important structural variation, the potentially biologically important structural variation is selected from one or more of a structural variation that resides in a gene in which less than 5% of normal individuals have a known structural variation; there is a custom correlation coefficient bloc in the gene; a frequency of the NMI at one site in the gene is greater than 5% in a diseased population; and there is a run of at least four SNPs with NMI in a row.