Patent Document ID: 9721062
Application ID: 15167530
Patent Flag: 1

Claim One:
1. A computer-based sequence analysis system comprising: a computer readable memory configured to store at least a first and a second genomic sequence datasets, the sequence datasets comprising genomic reads associated with respective first and second tissues; and a sequence analysis engine having a processor coupled with the computer readable memory and configured to: determine a common genomic location in the first and second genomic sequence datasets; generate at least a pair of pileups by: reading a first set of pileups that includes genomic reads from the first genomic sequence dataset and that overlap the common genomic location; and reading a second set of pileups that includes genomic reads from the second genomic sequence dataset and that also overlap the common genomic location; infer at least a pair of genotypes for the common genomic location based on the at least the pair of pileups, the at least the pair of genotypes including a first genotype associated with the first tissue and a second genotype associated with the second tissue; identify a genomic difference between the first genotype and the second genotype in the at least the pair of genotypes; filter false positives based on a skewing from a random distribution; and store the genomic difference in a device memory.