tstrait: a quantitative trait simulator for ancestral recombination graphs.
tstrait: a quantitative trait simulator for ancestral recombination graphs.
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tstrait：祖先重组图的数量性状模拟器。
DOI：
10.1101/2024.03.13.584790
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发表时间：
2024
期刊：
影响因子：
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通讯作者：
Kelleher,Jerome
中科院分区：
文献类型：
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作者：
Tagami,Daiki;Bisschop,Gertjan;Kelleher,Jerome
Ancestral重组图(ARGs)以紧凑和有效的结构编码由重组产生的相关系谱树的集合，在种群和统计遗传学中具有重要的基础作用。最近的突破使在生物库规模上模拟和推断ARG成为可能，现在人们对在广泛的应用中使用基于ARG的方法产生了浓厚的兴趣，特别是在全基因组关联研究(GWAS)中。使用群体遗传学模型模拟ARG的方法很复杂，但目前还没有软件可以直接从这些ARG模拟数量性状。要应用现有的数量性状模拟器，用户必须输出基因型数据，这会丢失有关祖先过程的重要信息，并且在应用于GWAS当前感兴趣的生物库规模的数据集时会产生令人望而却步的大文件。我们介绍了一个开源的Python库，用于模拟ARGs上的数量性状，并展示了这个用户友好的软件如何在笔记本电脑上快速模拟生物库规模的数据集的表型。Https://tskit.dev/tstrait/docs/，上提供了包含示例和工作流模板的完整文档，开发版本在GitHub(https://github.com/tskit-dev/tstrait).)上进行维护
SummaryAncestral recombination graphs (ARGs) encode the ensemble of correlated genealogical trees arising from recombination in a compact and efficient structure and are of fundamental importance in population and statistical genetics. Recent breakthroughs have made it possible to simulate and infer ARGs at biobank scale, and there is now intense interest in using ARG-based methods across a broad range of applications, particularly in genome-wide association studies (GWAS). Sophisticated methods exist to simulate ARGs using population genetics models, but there is currently no software to simulate quantitative traits directly from these ARGs. To apply existing quantitative trait simulators users must export genotype data, losing important information about ancestral processes and producing prohibitively large files when applied to the biobank-scale datasets currently of interest in GWAS. We presenttstrait, an open-source Python library to simulate quantitative traits on ARGs, and show how this user-friendly software can quickly simulate phenotypes for biobank-scale datasets on a laptop computer.Availability and implementationtstraitis available for download on the Python Package Index. Full documentation with examples and workflow templates is available on https://tskit.dev/tstrait/docs/, and the development version is maintained on GitHub (https://github.com/tskit-dev/tstrait).