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affy2sv: an R package to pre-process Affymetrix CytoScan HD and 750K arrays for SNP, CNV, inversion and mosaicism calling. Hernandez-Ferrer, Carles, 1987- Quintela Garcia, Ines Danielski, Katharina Carracedo, Ángel Pérez Jurado, Luis Alberto González Ruiz, Juan Ramón Genoma humà Oligonucleòtids Background:The well-known Genome-Wide Association Studies (GWAS) had led to many scientific discoveriesusing SNP data. Even so, they were not able to explain the full heritability of complex diseases. Now, other structuralvariants like copy number variants or DNA inversions, either germ-line or in mosaicism events, are being studies.We present the R packageaffy2svto pre-process Affymetrix CytoScan HD/750k array (also for Genome-WideSNP 5.0/6.0 and Axiom) in structural variant studies.Results:We illustrate the capabilities ofaffy2svusing two different complete pipelines on real data. The firstone performing a GWAS and a mosaic alterations detection study, and the other detecting CNVs and performingan inversion calling.Conclusion:Both examples presented in the article show up howaffy2svcan be used as part of more complexpipelines aimed to analyze Affymetrix SNP arrays data in genetic association studies, where different types ofstructural variants are considered. This work was partly supported by the Spanish Ministry of Science and Innovation (MTM2011-26515), FIS PI1002512 and a predoctoral fellowship of the Universitat Pompeu Fabra (to CH-F). 2015-10-15T11:22:48Z 2015-10-15T11:22:48Z 2015 info:eu-repo/semantics/article info:eu-repo/semantics/publishedVersion Hernandez-Ferrer C, Quintela Garcia I, Danielski K, Carracedo Á, Pérez-Jurado LA, González JR. affy2sv: an R package to pre-process Affymetrix CytoScan HD and 750K arrays for SNP, CNV, inversion and mosaicism calling. BMC Bioinformatics. 2015 May 20;16:167. DOI: 10.1186/s12859-015-0608-y. 1471-2105 http://hdl.handle.net/10230/24848 http://dx.doi.org/10.1186/s12859-015-0608-y eng BMC Bioinformatics. 2015 May 20;16:167 info:eu-repo/grantAgreement/ES/3PN/MTM2011-26515 © 2015 Hernandez-Ferrer et al.; licensee BioMed Central. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0), which permits unrestricted use,/ndistribution, and reproduction in any medium, provided the original work is properly credited. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated. http://creativecommons.org/licenses/by/4.0/ info:eu-repo/semantics/openAccess application/pdf application/pdf BioMed Central