SNPator (SNP Analysis to Results)
The Very Basics:
SNPator is a web-based environment oriented towards Statistical Genomics Analysis. It
focuses on large sets of SNP data such as those generated by high-throughput genotyping
SNPator has been designed to help users store, handle, retrieve, transform and analyze their data. To that end, SNPator allows you to perform an increasingly large set of operations.
They range from format transformations (e.g. creating input files that are ready to use in
your favorite analysis software) and quality controls to complex Statistical Genomics
calculations such as association tests or haplotype inference.
In some cases, SNPator uses some algorithms written from scratch in PHP or R, in other
cases, calculations are performed by standard software packages, such as Arlequin (Scheneider et al. 2000) or Phase (Stephens et al. 2001; Stephens and Donnelly 2003),
running in dedicated servers. Of course, we only run software on a strictly legal basis and in
strict agreement with the license terms. For a package to be supported by SNPator it needs to
be free for non-commercial use.
The development of SNPator has been funded by Genoma España within the CeGen
(Centro Nacional de Genotipado) project.
As a part of CeGen's Central Node, located in the Universitat Pompeu Fabra (UPF,
Barcelona), CeGen's Bioinformatics Division is mainly oriented to provide services for CeGen users. SNPator is designed to that end.
The team building and maintaining SNPator is directed by Arcadi Navarro and currently
involves three great people: Carlos Morcillo (Project Manager), Pep Alegre (Senior
Programmer) and Ricard Sangrós (Programmer), all of them in the UPF. Francesc Calafell, also in the UPF, works closely with the team.
SNPator also benefits from valuable feedback provided by many of its users. All the people
involved in the CeGen project should be thanked. Special credit should be given to Elena
Bosch, Ferran Casals, Anna Ferrer and Andrés Moreno in the UPF, and to Mònica
and Rafa de Cid, in the Centre de Regulació Genòmica (CRG, Barcelona), for patiently
testing SNPator's functionalities and coming up with brilliant ideas. Jorge Amigo, in the
Universidade de Santiago de Compostela (USC, Santiago) provided helpful feedback for
the Quality Control processes. Anna González, Joaquín Dopazo, Patricio Traverso and Roger Milne in the Centro Nacional de Investigaciones Oncológicas (CNIO, Madrid) also
provided important feedback.
Last, but not least, Jaume Bertranpetit (CeGen's Coordinator) has to be thanked for
continually working to keep SNPator alive.
- Schneider, S.,Roessli, D., and Excoffier, L. (2000) Arlequin: A software for population
genetics data analysis. Ver 2.000. Genetics and Biometry Lab, Dept. of Anthropology,
University of Geneva.
- Stephens, M., and Donnelly, P. (2003). A comparison of Bayesian
methods for haplotype
reconstruction from population genotype data. American Journal of Human Genetics,