School of Medicine, Ningbo University, Ningbo 315211, China.
Genomics Proteomics Bioinformatics. 2010 Dec;8(4):268-73. doi: 10.1016/S1672-0229(10)60029-0.
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.
高通量基因分型芯片为全基因组关联研究 (GWAS) 产生了庞大的数据集，为发现复杂疾病的易感性基因做出了巨大贡献。GWAS 的数据分析有两种策略。一种策略是使用专为 GWAS 设计的开源或商业软件包。另一种是利用具有特定功能的经典遗传程序，如连锁不平衡映射、单倍型推断和传递不平衡检验。然而，大多数现有的经典程序并不适合直接分析芯片数据，需要定制输入，这导致将原始基因分型文件转换为各种数据格式很不方便。我们开发了一个名为 SNPTransformer 的功能强大、用户友好、轻量级的 GWAS 程序，它包含五个主要模块（Transformer、Operator、Previewer、Coder 和 Simulator）。该工具包不仅可以将基因分型文件转换为十种输入格式，以用于经典遗传学软件包，还可以执行有用的功能，如对 ID 进行关系操作、预览数据文件、重新编码数据格式和模拟标记文件等。它连接了上游的原始基因分型数据和下游的遗传程序，可作为人类遗传学家的实用工具包，特别是对于非程序员。SNPTransformer 可在 http://snptransformer.sourceforge.net 免费获得。
