GDF a HighThroughput Multiplatform Genotyping Filter Jorge AmigoLechuga

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GDF: a High-Throughput Multiplatform Genotyping Filter Jorge Amigo-Lechuga and Ángel Carracedo Legal Medicine Institute

GDF: a High-Throughput Multiplatform Genotyping Filter Jorge Amigo-Lechuga and Ángel Carracedo Legal Medicine Institute (University of Santiago de Compostela) National Genotyping Centre of Spain Description: The Genotyping Data Formatter (GDF) is a program written in perl that is able to deal with data coming from any genotyping platform (Sequenom and SNPlex are already considered, and we are currently working on Illumina and Taqman), and allows users to obtain added value to their data. The two main benefits are: - Quick consistency and error checking of the obtained genotypes when working with large amounts of data - Precise data parsing into any desired format to work later with specific analysis software Genotyping Platforms Automated Data Reading and Pre-Analysis Sequenom Data management Analysis (Arlequin, Phase, Haploview, …) GDF Storage (SNPator) SNPlex Integration: The data flow on the left shows how GDF reads the genotyped data coming from the available platforms and process it for its storage and/or its use in any software for deeper data studies. Input: The GDF web interface is available through http: //bioinformatics. cesga. es/, and allows researchers and technicians not only to enter the data coming from the genotyping platforms but to give additional information like pedigree, a short snp description (gene name and snp position) or allele translation information. Formatting: GDF is able to modify the genotyped data in order to provide the input for specific analysis software. The avalilable programs are Arlequin, Phase, EMLD, Hapblock, Haploview, Unphased and MDR. Output: The results obtained are some statistics and a summary of the genotyped data. Their combination provide the user with relevant information such as third alleles, failed genotypes location on plates or missmatching duplications. Access: The web access of GDF is the most used, but it is also capable of running in command line, and so it can be integrated in bigger software developments. A current integration example is its data parsing and importing role in the SNPator database of the Bioinformatics division of the Spanish National Genotyping Centre. Acknowledgements: To Javier Costas, Iván Cristobo, María Torres, Bea Sobrino, María Brión, Chris Phillips and Francisco Barros.