ChopSticks: High-resolution analysis of homozygous deletions by exploiting concordant read pairs.

ABSTRACT:

Background

Structural variations (SVs) in genomes are commonly observed even in healthy individuals and play key roles in biological functions. To understand their functional impact or to infer molecular mechanisms of SVs, they have to be characterized with the maximum resolution. However, high-resolution analysis is a difficult task because it requires investigation of the complex structures involved in an enormous number of alignments of next-generation sequencing (NGS) reads and genome sequences that contain errors.

Results

We propose a new method called ChopSticks that improves the resolution of SV detection for homozygous deletions even when the depth of coverage is low. Conventional methods based on read pairs use only discordant pairs to localize the positions of dele

SUBMITTER: Yasuda T 

PROVIDER: S-EPMC3582528 | biostudies-literature | 2012 Oct

REPOSITORIES: biostudies-literature