CNVRuler: a copy number variation-based case–control association analysis tool | Zendy

Ji Hong Kim | Zendy; HaeJin Hu | Zendy; SeonHee Yim | Zendy; Joon Seol Bae | Zendy; Seon Young Kim | Zendy; YeunJun Chung | Zendy

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

Author(s) -

Ji Hong Kim,

HaeJin Hu,

SeonHee Yim,

Joon Seol Bae,

Seon Young Kim,

YeunJun Chung

Publication year - 2012

Publication title -

bioinformatics

Language(s) - English

Resource type - Journals

eISSN - 1367-4811

pISSN - 1367-4803

DOI - 10.1093/bioinformatics/bts239

Subject(s) - population stratification , genome wide association study , copy number variation , computer science , java , snp , genetic association , association (psychology) , software , variation (astronomy) , single nucleotide polymorphism , computational biology , biology , genetics , programming language , genome , psychology , genotype , physics , gene , astrophysics , psychotherapist

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.

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