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© Xavier Montagutelli, Institut Pasteur
Publication : G3 (Bethesda, Md.)

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

Scientific Fields
Diseases
Organisms
Applications
Technique

Published in G3 (Bethesda, Md.) - 04 Nov 2022

Bourdon M, Montagutelli X

Link to Pubmed [PMID] – 36000885

Link to DOI – 10.1093/g3journal/jkac219

G3 (Bethesda) 2022 Nov; 12(11):

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/.