GASP -- a software tool for methodologic development in

基因分析模拟程序（G.A.S.P.）是一个软件工具，用于生成基于用户指定的遗传模型的家庭数据样本。数量性状是根据用户定义成分的组合来定义的，包括一个主位点（或多个位点）、一个多基因成分、共同的兄弟姐妹环境和/或其他协变量。此外，还可以生成与离散性状或标记相对应的位点。然而，诸如数据缺失、基因分型错误、外显率降低、遗传异质性、上位性和非随机确定等并发症并不是由该软件直接处理的。G.A.S.P.与驱动程序一起运行，驱动程序对生成的数据进行格式化，也可以用来为模型增加复杂的层次。基于驱动的性状修改包括：功能转换，根据阈值对数量性状进行分类，以及随机确定离散性状的表达（降低外显率）。更复杂的性状模型允许一个位点的贡献取决于另一个位点的基因型。非随机确定可以通过丢弃不符合期望标准的家庭来建模。驱动程序可以允许混合种群，建模部分关联或遗传异质性，通过为每个种群维护单独的模型规范和随机数流，并以期望的比例包括来自不同种群的家庭。大多数模拟研究需要从所考虑的每个总体模型中使用数千个样本。生成数据、调用分析程序、提取相关输出以及为每个复制积累结果都是必要的。使用unix shell脚本与G.A.S.P.和适当的驱动程序相结合来完成这些任务。

The Genometric Analysis Simulation Program (G.A.S.P.) is a software tool for generating samples of family data based on user-specified genetic models. Quantitative traits are defined in terms of a combination of user-defined components, including a major-locus (or loci), a polygenic component, common sibship environment, and/or other covariates. In addition, loci corresponding to discrete traits or markers can be generated. However, complications such as missing data, genotyping errors reduced penetrance, genetic heterogeneity, epistasis, and non-random ascertainment are not handled directly by this software. G.A.S.P. is run in combination with a driver that formats the generated data and can also be used to add layers of complexity to the mdoel. Driver-based trait modifications include: functional transformation, classification of a quantitative trait according to a threshold, and randomly determined expression of a discrete trait (reduced penetrance). More complicated trait models allow for the contribution of one locus to depend on the genotype at another locus. Non-random ascertainment can be modeled by discarding families that do not meet the desired criterion. The driver can allow for mixtures of populations, modeling partial association or genetic heterogeneity, by maintaining separate model specifications and random number streams for each population and including families from different populations in the desired proportions. Most simulation studies require the use of thousands of samples from each population model considered. It is necessary to generate data, invoke analysis programs, extract relevant output, and accumulate results for each replicate. A unix shell script is used in combination with G.A.S.P. and appropriate driver programs to accomplish these tasks.