A robust model for read count data in exome sequencing experiments and implications for copy number variant calling.

ABSTRACT:

Motivation

Exome sequencing has proven to be an effective tool to discover the genetic basis of Mendelian disorders. It is well established that copy number variants (CNVs) contribute to the etiology of these disorders. However, calling CNVs from exome sequence data is challenging. A typical read depth strategy consists of using another sample (or a combination of samples) as a reference to control for the variability at the capture and sequencing steps. However, technical variability between samples complicates the analysis and can create spurious CNV calls.

Results

Here, we introduce ExomeDepth, a new CNV calling algorithm designed to control for this technical variability. ExomeDepth uses a robust model for the read count data and uses this model to build an optimized ref

SUBMITTER: Plagnol V 

PROVIDER: S-EPMC3476336 | biostudies-literature | 2012 Nov

REPOSITORIES: biostudies-literature