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).