Abstract
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.
Highlights
For over fifty years, “traditional” livestock breeding has combined phenotypes and statistical models to infer the genetic value of individuals
single nucleotide polymorphism (SNP) array technology revolutionized this scenario for the animal genetics industry and research
Ease of installation and use is ensured by the fact that SNPConvert (GUI or source code) is multiplatform
Summary
“traditional” livestock breeding has combined phenotypes and statistical models to infer the genetic value of individuals. SNP array technology revolutionized this scenario for the animal genetics industry and research. For the first time, it was possible to obtain consistent and cost-effective genetic information directly from dense genome-wide markers. A review of the impact of the genomic revolution on domestic animals is presented in [1]. The interest raised towards such technology created new opportunities for companies providing these service (e.g., Illumina and Affymetrix). A large series of products were produced to fit market requests. A wide variety of low-, medium- and high-density
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