SNPConvert: SNP Array Standardization and Integration in Livestock Species.
One of the main advantages of single nucleotide polymorphism (SNP) array technology is providing genotype calls for a specific number of SNP markers at a relatively low cost. Since its first application in animal genetics, the number of available SNP arrays for each species has been constantly increasing. However, conversely to that observed in whole genome sequence data analysis, SNP array data does not have a common set of file formats or coding conventions for allele calling. Therefore, the standardization and integration of SNP array data from multiple sources have become an obstacle, especially for users with basic or no programming skills. Here, we describe the difficulties related to handling SNP array data, focusing on file formats, SNP allele coding, and mapping. We also present SNPConvert suite, a multi-platform, open-source, and user-friendly set of tools to overcome these issues. This tool, which can be integrated with open-source and open-access tools already available, is a first step towards an integrated system to standardize and integrate any type of raw SNP array data. The tool is available at: https://github. com/nicolazzie/SNPConvert.git.
Bioinformatics Core Facility, PTP Science Park, Via Einstein-Loc. Cascina Codazza 26900 Lodi, Italy. ezequiel.nicolazzi@ptp.it.
Ezequiel Luis
EL
Nicolazzi
Bioinformatics Core Facility, PTP Science Park, Via Einstein-Loc. Cascina Codazza 26900 Lodi, Italy. gabriele.marras@ptp.it.
Gabriele
G
Marras
Bioinformatics Core Facility, PTP Science Park, Via Einstein-Loc. Cascina Codazza 26900 Lodi, Italy. stella@ibba.cnr.it.|Istituto di Biologia e Biotecnologia Agraria-Consiglio Nazionale della Ricerca, Via Einstein-Loc. Cascina Codazza 26900 Lodi, Italy. stella@ibba.cnr.it.
Alessandra
A
Stella
array; integration; single nucleotide polymorphism; software; standardization