BIOINFORMATICS SYSTEMS, APPARATUSES, AND METHODS FOR PERFORMING SECONDARY AND/OR TERTIARY PROCESSING

A system, method and acomputer-readable storage device for improving the accuracy of a variant call by jointly evaluating reads that map to two or more regions of a reference sequence that are homologous are disclosed. The method comprises accessing a joint-pileup including a first pileup of sequence reads that have been aligned to a first region of the reference sequence and at least a second pileup of reads that have been aligned to a second region of the reference sequence, wherein the first region and the second region are homologous with each other; determining a set of candidate variants from the joint-pileup; defining a connection matrix that defines an order of processing of the candidate variants; evaluating, by the one or more computers, each of the candidate variants from the set of candidate variants based on the defined processing order; and generating variant call file that identifies one or more of the candidate variants.