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. 2016 Jun 9;5(2):17.
doi: 10.3390/microarrays5020017.

SNPConvert: SNP Array Standardization and Integration in Livestock Species

Ezequiel Luis Nicolazzi  1 , Gabriele Marras  2 , Alessandra Stella  3   4
Affiliations

SNPConvert: SNP Array Standardization and Integration in Livestock Species

Ezequiel Luis Nicolazzi et al. Microarrays (Basel). .

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.

Keywords: array; integration; single nucleotide polymorphism; software; standardization.

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Figures

Figure 1
Figure 1
Flowchart of SNPConvert functionalities for files in Illumina row, matrix, or PLINK file format. Dashed lines indicate optional steps. Pointed boxes indicate interactions with third-party software.
See this image and copyright information in PMC

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