CnvOffSeq: detecting intergenic copy number variation using off-target exome sequencing data.

ABSTRACT:

Motivation

Exome sequencing technologies have transformed the field of Mendelian genetics and allowed for efficient detection of genomic variants in protein-coding regions. The target enrichment process that is intrinsic to exome sequencing is inherently imperfect, generating large amounts of unintended off-target sequence. Off-target data are characterized by very low and highly heterogeneous coverage and are usually discarded by exome analysis pipelines. We posit that off-target read depth is a rich, but overlooked, source of information that could be mined to detect intergenic copy number variation (CNV). We propose cnvOffseq, a novel normalization framework for off-target read depth that is based on local adaptive singular value decomposition (SVD). This method is designed to a

SUBMITTER: Bellos E 

PROVIDER: S-EPMC4147927 | biostudies-literature | 2014 Sep

REPOSITORIES: biostudies-literature