SNPTransformer:A Lightweight Toolkit for Genome-Wide Association Studies

作     者：Changzheng Dong 

作者机构：School of Medicine Ningbo University Ningbo 315211 China 

出 版 物：《Genomics, Proteomics & Bioinformatics》 (基因组蛋白质组与生物信息学报（英文版）)

年 卷 期：2010年第8卷第4期

页      面：268-273页

核心收录：

学科分类：0710[理学-生物学] 07[理学] 08[工学] 09[农学] 071007[理学-遗传学] 0835[工学-软件工程] 0901[农学-作物学] 0836[工学-生物工程] 090102[农学-作物遗传育种] 081202[工学-计算机软件与理论] 0812[工学-计算机科学与技术（可授工学、理学学位）] 

基　　金：supported by Zhejiang Provincial Natural Science Foundation (No. Y2100240) Ningbo Natural Science Foundation (No. 2009A610142) Zhejiang Provincial Health Department Foundation (No. 2009A183) the Hulan Scholar Fund and the K.C. Wong Magna Fund at Ningbo University 

主　　题：genome-wide association studies tool genotyping files conversion 

摘      要：High-throughput genotyping chips have produced huge datasets for genome-wide association studies （GWAS） that have contributed greatly to discovering susceptibility genes for complex diseases. There are two strategies for performing data analysis for GWAS. One strategy is to use open-source or commercial packages that are designed for GWAS. The other is to take advantage of classic genetic programs with specific functions, such as linkage disequilibrium mapping, haplotype inference and transmission disequilibrium tests. However, most classic programs that are available are not suitable for analyzing chip data directly and require custom-made input, which results in the inconvenience of converting raw genotyping files into various data formats. We developed a powerful, user-friendly, lightweight program named SNPTransformer for GWAS that includes five major modules （Transformer, Operator, Previewer, Coder and Simulator）. The toolkit not only works for transforming the genotyping files into ten input formats for use with classic genetics packages, but also carries out useful functions such as relational operations on IDs, previewing data files, recoding data formats and simulating marker files, among other functions. It bridges upstream raw genotyping data with downstream genetic programs, and can act as an in-hand toolkit for human geneticists, especially for non-programmers. SNPTransformer is freely available at http：//***.