Improving somatic variant identification through integration of genome and exome data

Cost-effective high-throughput sequencing technologies, together with efficient mapping and variant calling tools, have made it possible to identify somatic variants for cancer study. However, integrating somatic variants from whole exome and whole genome studies poses a challenge to researchers as the variants identified by whole genome analysis may not be identified by whole exome analysis and vice versa. Simply taking the union or intersection of the results may lead to too many false positives or too many false negatives.