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://snptransformer.sourceforge.net.