stuart：用于实验杂交中 SNP 基因型编纂的 R 包。

stuart: an R package for the curation of SNP genotypes from experimental crosses.

机构信息

Mouse Genetics Laboratory, Institut Pasteur, Université Paris Cité, F-75015 Paris, France.

出版信息

G3 (Bethesda). 2022 Nov 4;12(11). doi: 10.1093/g3journal/jkac219.

DOI:10.1093/g3journal/jkac219

PMID:36000885

原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC9635635/

Abstract

Genetic mapping in 2-generation crosses requires genotyping, usually performed with single nucleotide polymorphism markers arrays which provide high-density genetic information. However, genetic analysis on raw genotypes can lead to spurious or unreliable results due to defective single nucleotide polymorphism assays or wrong genotype interpretation. Here, we introduce stuart, an open-source R package, which analyzes raw genotyping data to filter single nucleotide polymorphism markers based on informativeness, Mendelian inheritance pattern, and consistency with parental genotypes. The functions of this package provide a curation pipeline and formatting adequate for genetic analysis with the R/qtl package. stuart is available with detailed documentation from https://gitlab.pasteur.fr/mouselab/stuart/.

摘要

在 2 代杂交中进行遗传图谱构建需要进行基因型鉴定，通常使用单核苷酸多态性标记阵列来进行，因为它可以提供高密度的遗传信息。然而，由于单核苷酸多态性检测的缺陷或基因型解释错误，原始基因型的遗传分析可能会导致虚假或不可靠的结果。在这里，我们介绍了一个开源的 R 包 stuart，它可以分析原始的基因分型数据，根据信息量、孟德尔遗传模式和与亲本基因型的一致性来过滤单核苷酸多态性标记。该软件包的功能提供了一个策展管道和格式化，以适应与 R/qtl 软件包进行遗传分析。stuart 可以从 https://gitlab.pasteur.fr/mouselab/stuart/ 获取详细文档。