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Bioinformatics Advance Access originally published online on May 30, 2008
Bioinformatics 2008 24(14):1643-1644; doi:10.1093/bioinformatics/btn241
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© The Author 2008. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

SNP analysis to results (SNPator): a web-based environment oriented to statistical genomics analyses upon SNP data

Carlos Morcillo-Suarez 1,2,3, Josep Alegre 1,2,3, Ricardo Sangros 1,2,3, Elodie Gazave 1, Rafael de Cid 2,4, Roger Milne 2,5, Jorge Amigo 2,6, Anna Ferrer-Admetlla 1, Andrés Moreno-Estrada 1, Michelle Gardner 1, Ferran Casals 1, Anna Pérez-Lezaun 1,2, David Comas 1,7, Elena Bosch 1,7, Francesc Calafell 1,7, Jaume Bertranpetit 1,2,7 and Arcadi Navarro 1,2,3,7,8,*

1Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, Barcelona Biomedical Research Park (PRBB), Barcelona, 2National Genotyping Centre (CeGen), 3Population Genomics Node (GNV8) National Institute for Bioinformatics (INB), 4Genes and Disease Program, Center for Genomic Regulation (CRG), Barcelona, 5Human Genetics Group, Human Cancer Genetics Program, Spanish National Cancer Centre, Madrid, 6Unidade de Xenética, Facultad de Medicina, Santiago de Compostela, 7CIBER en Epidemiologia y Salud Pública (CIBERESP) and 8Institució Catalana de Recerca i Estudis Avançats, ICREA and Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, Dr Aiguader 88, 08003 Barcelona, Spain

*To whom correspondence should be addressed.


  Abstract

Summary: Single nucleotide polymorphisms (SNPs) are the most widely used marker in studies to assess associations between genetic variants and complex traits or diseases. They are also becoming increasingly important in the study of the evolution and history of humans and other species. The analysis and processing of SNPs obtained thanks to high-throughput technologies imply the time consuming and costly use of different, complex and usually format-incompatible software. SNPator is a user-friendly web-based SNP data analysis suite that integrates, among many other algorithms, the most common steps of a SNP association study. It frees the user from the need to have large computer facilities and an in depth knowledge of genetic software installation and management. Genotype data is directly read from the output files of the usual genotyping platforms. Phenotypic data on the samples can also be easily uploaded. Many different quality control and analysis procedures can be performed either by using built-in SNPator algorithms or by calling standard genetic software.

Availability: Access is granted from the SNPator webpage http://www.snpator.org.

Contact: arcadi.navarro{at}upf.edu; bioinformatica.cegen{at}upf.edu

Supplementary information: Additional information, including tutorials and example datasets, is available from SNPator's webpage.

Associate Editor: Martin Bishop

Received on February 21, 2008; revised on May 16, 2008; accepted on May 16, 2008

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