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. Other structural variants like copy number variants or DNA inversions, either germ-line or in mosaicism events, are being studies.
affy2sv is an R package to pre-process Affymetrix CytoScan HD/750k array (also for Genome-Wide SNP 5.0/6.0 and Axiom) in structural variant studies.
The R package is available at Bitbucket:
The project resulted in a publication at BMC Bioinformatics (Open Access):
affy2sv: an R package to pre-process Affymetrix CytoScan HD and 750K arrays for SNP, CNV, inversion and mosaicism calling
Carles Hernandez-Ferrer, Ines Quintela Garcia, Katharina Danielski, Angel Carracedo, Luis A. Perez-Jurado and Juan R. Gonzalez / BMC Bioinformatics 2015 / doi:10.1186/s12859-015-0608-y
The report of the project and the slides used in the academic defense follows of my master’s project: