DEFOR: Depth- and frequency-based somatic copy number alteration detector

Motivation: Detection of somatic copy number alterations (SCNAs) using high-throughput sequencing has become popular because of rapid developments in sequencing technology. Existing methods do not perform well in calling SCNAs for the unstable tumor genomes. Results: We developed a new method, DEFOR, to detect SCNAs in tumor samples from exome-sequencing data. The evaluation showed that DEFOR has a higher accuracy for SCNA detection from exome sequencing compared with the five existing tools. This advantage is especially apparent in unstable tumor genomes with a large proportion of SCNAs. Availability and implementation: DEFOR is available at https://github.com/drzh/defor. Supplementary information: Supplementary data are available at Bioinformatics online.