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Dong C. SNPTransformer: a lightweight toolkit for genome-wide association studies. Genomics Proteomics Bioinformatics. 2010;8(4):268-73doi: 10.1016/S1672-0229(10)60029-0.
Dong, C. (2010). SNPTransformer: a lightweight toolkit for genome-wide association studies. Genomics, proteomics & bioinformatics, 8(4), 268-73. https://doi.org/10.1016/S1672-0229(10)60029-0
Dong, Changzheng. "SNPTransformer: a lightweight toolkit for genome-wide association studies." Genomics, proteomics & bioinformatics vol. 8,4 (2010): 268-73. doi: https://doi.org/10.1016/S1672-0229(10)60029-0
Dong C. SNPTransformer: a lightweight toolkit for genome-wide association studies. Genomics Proteomics Bioinformatics. 2010 Dec;8(4):268-73. doi: 10.1016/S1672-0229(10)60029-0. PMID: 21382596; PMCID: PMC5054149.
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Genomics Proteomics Bioinformatics. 2010 Dec;8(4):268-73. doi: 10.1016/S1672-0229(10)60029-0.

SNPTransformer: a lightweight toolkit for genome-wide association studies.

Genomics, proteomics & bioinformatics

Changzheng Dong

Affiliations

  1. School of Medicine, Ningbo University, Ningbo 315211, China. [email protected]

PMID: 21382596 PMCID: PMC5054149 DOI: 10.1016/S1672-0229(10)60029-0

Abstract

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.

Copyright © 2010 Beijing Genomics Institute. Published by Elsevier Ltd. All rights reserved.

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