QCGWAS: A flexible R package for automated quality control of genome-wide association results

被引：18

作者：

van der Most, Peter J. ^{[1
]}

Vaez, Ahmad ^{[1
]}

Prins, Bram P. ^{[1
,2
]}

Munoz, M. Loretto ^{[1
]}

Snieder, Harold ^{[1
]}

Alizadeh, Behrooz Z. ^{[1
]}

Nolte, Ilja M. ^{[1
]}

机构：

[1] Univ Groningen, Univ Med Ctr Groningen, Dept Epidemiol, NL-9700 RB Groningen, Netherlands

[2] St George Hosp, Sch Med, Human Genet Res Ctr, Cardiogenet Lab, London SW17 0RE, England

来源：

BIOINFORMATICS | 2014年 / 30卷 / 08期

关键词：

METAANALYSIS;

D O I：

10.1093/bioinformatics/btt745

中图分类号：

Q5 [生物化学];

学科分类号：

071010 ; 081704 ;

摘要：

QCGWAS is an R package that automates the quality control of genome-wide association result files. Its main purpose is to facilitate the quality control of a large number of such files before meta-analysis. Alternatively, it can be used by individual cohorts to check their own result files. QCGWAS is flexible and has a wide range of options, allowing rapid generation of high-quality input files for meta-analysis of genome-wide association studies.

引用

页码：1185 / 1186

页数：2

共 12 条

[1] An integrated map of genetic variation from 1,092 human genomes [J].

Altshuler, David M. ;

Durbin, Richard M. ;

Abecasis, Goncalo R. ;

Bentley, David R. ;

Chakravarti, Aravinda ;

Clark, Andrew G. ;

Donnelly, Peter ;

Eichler, Evan E. ;

Flicek, Paul ;

Gabriel, Stacey B. ;

Gibbs, Richard A. ;

Green, Eric D. ;

Hurles, Matthew E. ;

Knoppers, Bartha M. ;

Korbel, Jan O. ;

Lander, Eric S. ;

Lee, Charles ;

Lehrach, Hans ;

Mardis, Elaine R. ;

Marth, Gabor T. ;

McVean, Gil A. ;

Nickerson, Deborah A. ;

Schmidt, Jeanette P. ;

Sherry, Stephen T. ;

Wang, Jun ;

Wilson, Richard K. ;

Gibbs, Richard A. ;

Dinh, Huyen ;

Kovar, Christie ;

Lee, Sandra ;

Lewis, Lora ;

Muzny, Donna ;

Reid, Jeff ;

Wang, Min ;

Wang, Jun ;

Fang, Xiaodong ;

Guo, Xiaosen ;

Jian, Min ;

Jiang, Hui ;

Jin, Xin ;

Li, Guoqing ;

Li, Jingxiang ;

Li, Yingrui ;

Li, Zhuo ;

Liu, Xiao ;

Lu, Yao ;

Ma, Xuedi ;

Su, Zhe ;

Tai, Shuaishuai ;

Tang, Meifang .

NATURE, 2012, 491 (7422) :56-65

[2] GenABEL: an R library for genome-wide association analysis [J].

Aulchenko, Yurii S. ;

Ripke, Stephan ;

Isaacs, Aaron ;

Van Duijn, Cornelia M. .

BIOINFORMATICS, 2007, 23 (10) :1294-1296

[3] Practical aspects of imputation-driven meta-analysis of genome-wide association studies [J].

de Bakker, Paul I. W. ;

Ferreira, Manuel A. R. ;

Jia, Xiaoming ;

Neale, Benjamin M. ;

Raychaudhuri, Soumya ;

Voight, Benjamin F. .

HUMAN MOLECULAR GENETICS, 2008, 17 :R122-R128

[4] Genomic control for association studies [J].

Devlin, B ;

Roeder, K .

BIOMETRICS, 1999, 55 (04) :997-1004

[5] GWAtoolbox: an R package for fast quality control and handling of genome-wide association studies meta-analysis data [J].

Fuchsberger, Christian ;

Taliun, Daniel ;

Pramstaller, Peter P. ;

Pattaro, Cristian .

BIOINFORMATICS, 2012, 28 (03) :444-445

[6] Meta-analysis and imputation refines the association of 15q25 with smoking quantity [J].

Liu, Jason Z. ;

Tozzi, Federica ;

Waterworth, Dawn M. ;

Pillai, Sreekumar G. ;

Muglia, Pierandrea ;

Middleton, Lefkos ;

Berrettini, Wade ;

Knouff, Christopher W. ;

Yuan, Xin ;

Waeber, Gerard ;

Vollenweider, Peter ;

Preisig, Martin ;

Wareham, Nicholas J. ;

Zhao, Jing Hua ;

Loos, Ruth J. F. ;

Barroso, Ines ;

Khaw, Kay-Tee ;

Grundy, Scott ;

Barter, Philip ;

Mahley, Robert ;

Kesaniemi, Antero ;

McPherson, Ruth ;

Vincent, John B. ;

Strauss, John ;

Kennedy, James L. ;

Farmer, Anne ;

McGuffin, Peter ;

Day, Richard ;

Matthews, Keith ;

Bakke, Per ;

Gulsvik, Amund ;

Lucae, Susanne ;

Ising, Marcus ;

Brueckl, Tanja ;

Horstmann, Sonja ;

Wichmann, H-Erich ;

Rawal, Rajesh ;

Dahmen, Norbert ;

Lamina, Claudia ;

Polasek, Ozren ;

Zgaga, Lina ;

Huffman, Jennifer ;

Campbell, Susan ;

Kooner, Jaspal ;

Chambers, John C. ;

Burnett, Mary Susan ;

Devaney, Joseph M. ;

Pichard, Augusto D. ;

Kent, Kenneth M. ;

Satler, Lowell .

NATURE GENETICS, 2010, 42 (05) :436-U75

[7] GWAMA: software for genome-wide association meta-analysis [J].

Magi, Reedik ;

Morris, Andrew P. .

BMC BIOINFORMATICS, 2010, 11

[8]

Pournelle G. H., 1953, Journal of Mammalogy, V34, P133, DOI 10.1890/0012-9658(2002)083[1421:SDEOLC]2.0.CO

[9]

[10] PLINK: A tool set for whole-genome association and population-based linkage analyses [J].

Purcell, Shaun ;

Neale, Benjamin ;

Todd-Brown, Kathe ;

Thomas, Lori ;

Ferreira, Manuel A. R. ;

Bender, David ;

Maller, Julian ;

Sklar, Pamela ;

de Bakker, Paul I. W. ;

Daly, Mark J. ;

Sham, Pak C. .

AMERICAN JOURNAL OF HUMAN GENETICS, 2007, 81 (03) :559-575

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