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Bioinformatics. 2012 Jul 1;28(13):1790-2. doi: 10.1093/bioinformatics/bts239. Epub 2012 Apr 25.

CNVRuler: a copy number variation-based case-control association analysis tool.

Author information

1
Integrated Research Center for Genome Polymorphism, Department of Microbiology, School of Medicine, Catholic University of Korea, Seoul 137-701, Korea.

Abstract

SUMMARY:

The method for genome-wide association study (GWAS) based on copy number variation (CNV) is not as well established as that for single nucleotide polymorphism (SNP)-GWAS. Although there are several tools for CNV association studies, most of them do not provide appropriate definitions of CNV regions (CNVRs), which are essential for CNV-association studies. Here we present a user-friendly program called CNVRuler for CNV-association studies. Outputs from the 10 most common CNV defining algorithms can be directly used as input files for determining the three different definitions of CNVRs. Once CNVRs are defined, CNVRuler supports four kinds of statistical association tests and options for population stratification. CNVRuler is based on the open-source programs R and Java from Sun Microsystems.

AVAILABILITY:

CNVRuler software is available with an online manual at the website, www.ircgp.com/CNVRuler/index.html.

PMID:
22539667
DOI:
10.1093/bioinformatics/bts239
[Indexed for MEDLINE]

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