GW-CALL: Accurate Genome-Wide Variant Caller

Abstract

The main challenge in reliable variant calling using DNA reads is to extract information from reads mappable to multiple locations on the reference genome. Conventional approaches ignore these reads and rely on reads mappable uniquely to the reference genome. These approaches fail to perform satisfactorily in variant calling within repeat regions which are abundant in many species including homo sapiens. This, in turn, lowers the reliability of any downstream analysis including poor performance in genome-wide association studies. GW-CALL, a fast and accurate variant caller, is proposed. GW-CALL exploits information of all reads in a genome-wide decision making process. In particular, it partitions the genome into several independent regions called clusters and incorporates an efficient algorithm to use all reads belonging to a cluster in calling variants within that cluster.\n\nAvailabilityGW-CALL is implemented in C++ and is freely available at URL: brl.ce.sharif.edu/gwcall.