He Zhang1, Xiaowei Zhan1, James Brugarolas2, Yang Xie1,2. 1. Department of Clinical Sciences, University of Texas Southwestern Medical Center, Dallas, TX, USA. 2. Department of Internal Medicine and Kidney Cancer Program, Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX, USA.
Abstract
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.
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.
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