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CNView: a visualization and annotation tool for copy number variation from whole-genome sequencing

By Ryan L. Collins, Matthew R Stone, Harrison Brand, Joseph T Glessner, Michael E. Talkowski

Posted 20 Apr 2016
bioRxiv DOI: 10.1101/049536

Summary: Copy number variation (CNV) is a major component of structural differences between individual genomes. The recent emergence of population-scale whole-genome sequencing (WGS) datasets has enabled genome-wide CNV delineation. However, molecular validation at this scale is impractical, so visualization is an invaluable preliminary screening approach when evaluating CNVs. Standardized tools for visualization of CNVs in large WGS datasets are therefore in wide demand. Methods & Results: To address this demand, we developed a software tool, CNView, for normalized visualization, statistical scoring, and annotation of CNVs from population-scale WGS datasets. CNView surmounts challenges of sequencing depth variability between individual libraries by locally adapting to cohort-wide variance in sequencing uniformity at any locus. Importantly, CNView is broadly extensible to any reference genome assembly and most current WGS data types. Availability and Implementation: CNView is written in R, is supported on OS X, MS Windows, and Linux, and is freely distributed under the MIT license. Source code and documentation are available from https://github.com/RCollins13/CNView Contact: talkowski@chgr.mgh.harvard.edu Supplementary Information: Supplementary data are available at Bioinformatics online.

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