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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...
Autores principales: | , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
MDPI
2016
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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. |
format | Online Article Text |
id | pubmed-5003493 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2016 |
publisher | MDPI |
record_format | MEDLINE/PubMed |
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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