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Bioinformatics. 2019 Aug 8. pii: btz632. doi: 10.1093/bioinformatics/btz632. [Epub ahead of print]

CNVRanger: association analysis of CNVs with gene expression and quantitative phenotypes.

Author information

1
Animal Breeding and Genomics, Wageningen University & Research, Wageningen, The Netherlands.
2
Swedish University of Agricultural Sciences, Uppsala, Sweden.
3
Graduate School of Public Health and Health Policy, City University of New York, New York, NY, USA.
4
Embrapa Pecuaria Sudeste, São Carlos, Brazil.
5
Animal Science Department, University of São Paulo, Piracicaba, Brazil.
6
Institute of Bioinformatics, Ludwig-Maximilians-Universität München, München, Germany.

Abstract

SUMMARY:

Copy number variation (CNV) is a major type of structural genomic variation that is increasingly studied across different species for association with diseases and production traits. Established protocols for experimental detection and computational inference of CNVs from SNP array and next-generation sequencing data are available. We present the CNVRanger R/Bioconductor package which implements a comprehensive toolbox for structured downstream analysis of CNVs. This includes functionality for summarizing individual CNV calls across a population, assessing overlap with functional genomic regions, and genome-wide association analysis with gene expression and quantitative phenotypes.

AVAILABILITY:

http://bioconductor.org/packages/CNVRanger.

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