Whole exome sequencing is currently a technology of choice in large-scale cancer genomics studies, where the priority is to identify cancer-associated variants in coding regions. We describe a method for estimating allele-specific copy number using whole exome sequencing data from tumor and matched normal.
"Allele-specific copy number estimation by whole exome sequencing." Ann. Appl. Stat. 11 (2) 1169 - 1192, June 2017. https://doi.org/10.1214/17-AOAS1043