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

Abstract

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/.