A computational method for detecting copy number variations using scale-space filtering.

ABSTRACT:

Background

As next-generation sequencing technology made rapid and cost-effective sequencing available, the importance of computational approaches in finding and analyzing copy number variations (CNVs) has been amplified. Furthermore, most genome projects need to accurately analyze sequences with fairly low-coverage read data. It is urgently needed to develop a method to detect the exact types and locations of CNVs from low coverage read data.

Results

Here, we propose a new CNV detection method, CNV_SS, which uses scale-space filtering. The scale-space filtering is evaluated by applying to the read coverage data the Gaussian convolution for various scales according to a given scaling parameter. Next, by differentiating twice and finding zero-crossing points, inflection point

SUBMITTER: Lee J 

PROVIDER: S-EPMC3637191 | biostudies-literature | 2013 Feb

REPOSITORIES: biostudies-literature