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