A tool for the detection of copy number aberrations from targeted sequencing. All currently available methods are based on exonic depth of coverage, and suffer from the problems that bait efficiencies are non-uniform and that exons are irregularly distributed over the genome. By exploiting the off-target sequence reads, CopywriteR bypasses these problems. It allows for extracting DNA copy number profiles of a high quality comparable to those of ‘dedicated’ techniques such as SNP array, arrayCGH and low-coverage whole-genome sequencing techniques.