Hernández Ferrer, CarlesQuintela García, InésDanielski, KatharinaPérez Jurado, Luís AlbertoGonzález, Juan R.Carracedo Álvarez, Ángel2020-06-172020-06-172015Hernandez-Ferrer, C., Quintela Garcia, I., Danielski, K. et al. affy2sv: an R package to pre-process Affymetrix CytoScan HD and 750K arrays for SNP, CNV, inversion and mosaicism calling. BMC Bioinformatics 16, 167 (2015). https://doi.org/10.1186/s12859-015-0608-y1471-2105http://hdl.handle.net/10347/23016Background The well-known Genome-Wide Association Studies (GWAS) had led to many scientific discoveries using SNP data. Even so, they were not able to explain the full heritability of complex diseases. Now, other structural variants like copy number variants or DNA inversions, either germ-line or in mosaicism events, are being studies. We present the R package affy2sv to pre-process Affymetrix CytoScan HD/750k array (also for Genome-Wide SNP 5.0/6.0 and Axiom) in structural variant studies. Results We illustrate the capabilities of affy2sv using two different complete pipelines on real data. The first one performing a GWAS and a mosaic alterations detection study, and the other detecting CNVs and performing an inversion calling. Conclusion Both examples presented in the article show up how affy2sv can be used as part of more complex pipelines aimed to analyze Affymetrix SNP arrays data in genetic association studies, where different types of structural variants are considered.eng© 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, distribution, 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 statedAffymetrixCytoScanCytoScan HDCytoScan 750kCNVInversionMosaicismStructural variantsjournal article10.1186/s12859-015-0608-yopen access