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DEFOR: depth- and frequency-based somatic copy number alteration detector.


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.

SUBMITTER: Zhang H 

PROVIDER: S-EPMC6761943 | biostudies-literature | 2019 Oct

REPOSITORIES: biostudies-literature

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DEFOR: depth- and frequency-based somatic copy number alteration detector.

Zhang He H   Zhan Xiaowei X   Brugarolas James J   Xie Yang Y  

Bioinformatics (Oxford, England) 20191001 19


<h4>Motivation</h4>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.<h4>Results</h4>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 exist  ...[more]

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