G2P：用于基因型模拟、表型模拟和功效评估的全基因组关联研究模拟工具。
G2P: a Genome-Wide-Association-Study simulation tool for genotype simulation, phenotype simulation and power evaluation.
机构信息
Electrical and Information Engineering College, Jilin Agricultural Science and Technology University, Jilin, China.
Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education & College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, China.
出版信息
Bioinformatics. 2019 Oct 1;35(19):3852-3854. doi: 10.1093/bioinformatics/btz126.
MOTIVATION
Plenty of Genome-Wide-Association-Study (GWAS) methods have been developed for mapping genetic markers that associated with human diseases and agricultural economic traits. Computer simulation is a nice tool to test the performances of various GWAS methods under certain scenarios. Existing tools are either inefficient in terms of computation and memory efficiency or inconvenient to use to simulate big, realistic genotype data and phenotype data to evaluate available GWAS methods.
RESULTS
Here, we present a GWAS simulation tool named G2P that can be used to simulate genotype data, phenotype data and perform power evaluation of GWAS methods. G2P is a user-friendly tool with all functions is provided in both graphical user interface and pipeline manners and it is available for Windows, Mac and Linux environments. Furthermore, G2P achieves maximum efficiency in terms of both memory usage and simulation speed; with G2P, the simulation of genotype data that includes 1 000 000 samples and 2 000 000 markers can be accomplished in 5 h.
AVAILABILITY AND IMPLEMENTATION
The G2P software, user manual, and example datasets are freely available at GitHub: https://github.com/XiaoleiLiuBio/G2P.
SUPPLEMENTARY INFORMATION
Supplementary data are available at Bioinformatics online.
动机
已经开发出许多全基因组关联研究（GWAS）方法来绘制与人类疾病和农业经济性状相关的遗传标记。计算机模拟是测试各种 GWAS 方法在特定场景下性能的一种很好的工具。现有的工具在计算和内存效率方面效率低下，或者不方便用于模拟大型、真实的基因型数据和表型数据来评估可用的 GWAS 方法。
结果
在这里，我们提出了一个名为 G2P 的 GWAS 模拟工具，可用于模拟基因型数据、表型数据并评估 GWAS 方法的功效。G2P 是一个用户友好的工具，其所有功能都以图形用户界面和管道方式提供，并且可用于 Windows、Mac 和 Linux 环境。此外，G2P 在内存使用和模拟速度方面都实现了最高效率；使用 G2P，模拟包含 100 万个样本和 200 万个标记的基因型数据可以在 5 小时内完成。
可用性和实现
G2P 软件、用户手册和示例数据集可在 GitHub 上免费获得：https://github.com/XiaoleiLiuBio/G2P。
补充信息
补充数据可在生物信息学在线获得。
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