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

Abstract

A 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.

Keywords

Copy number variation (CNV); structural genomic variation; SNP-arrays; next-generation sequencing data

Published in

Bioinformatics
2020, volume: 36, number: 3, pages: 972-973

SLU Authors

• Da Silva, Vinicius

  • Department of Animal Biosciences, Swedish University of Agricultural Sciences
    
  • Wageningen University & Research Centre (Wageningen UR)

• Johansson, Anna Maria

  • Department of Animal Biosciences, Swedish University of Agricultural Sciences
    

UKÄ Subject classification

Bioinformatics (Computational Biology)

Publication identifier

• DOI: https://doi.org/10.1093/bioinformatics/btz632

Permanent link to this page (URI)

https://res.slu.se/id/publ/101819