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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 incre...

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Autores principales: Nicolazzi, Ezequiel Luis, Marras, Gabriele, Stella, Alessandra
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2016
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5003493/
https://www.ncbi.nlm.nih.gov/pubmed/27600083
http://dx.doi.org/10.3390/microarrays5020017
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author Nicolazzi, Ezequiel Luis
Marras, Gabriele
Stella, Alessandra
author_facet Nicolazzi, Ezequiel Luis
Marras, Gabriele
Stella, Alessandra
author_sort Nicolazzi, Ezequiel Luis
collection PubMed
description 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.
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spelling pubmed-50034932016-09-06 SNPConvert: SNP Array Standardization and Integration in Livestock Species Nicolazzi, Ezequiel Luis Marras, Gabriele Stella, Alessandra Microarrays (Basel) Article 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. MDPI 2016-06-09 /pmc/articles/PMC5003493/ /pubmed/27600083 http://dx.doi.org/10.3390/microarrays5020017 Text en © 2016 by the authors; licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC-BY) license (http://creativecommons.org/licenses/by/4.0/).
spellingShingle Article
Nicolazzi, Ezequiel Luis
Marras, Gabriele
Stella, Alessandra
SNPConvert: SNP Array Standardization and Integration in Livestock Species
title SNPConvert: SNP Array Standardization and Integration in Livestock Species
title_full SNPConvert: SNP Array Standardization and Integration in Livestock Species
title_fullStr SNPConvert: SNP Array Standardization and Integration in Livestock Species
title_full_unstemmed SNPConvert: SNP Array Standardization and Integration in Livestock Species
title_short SNPConvert: SNP Array Standardization and Integration in Livestock Species
title_sort snpconvert: snp array standardization and integration in livestock species
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5003493/
https://www.ncbi.nlm.nih.gov/pubmed/27600083
http://dx.doi.org/10.3390/microarrays5020017
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