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

Abstract

Genetic mapping in two-generation crosses requires genotyping, usually performed with SNP markers arrays which provide high-density genetic information. However, genetic analysis on raw genotypes can lead to spurious or unreliable results due to defective SNP assays or wrong genotype interpretation. Here we introduce stuart, an open-source R package which analyzes raw genotyping data to filter SNP markers based on informativeness, Mendelian inheritance pattern and consistency with parental genotypes. 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/.