R/qtl2: Software for Mapping Quantitative Trait Loci with High-Dimensional Data and Multiparent Populations

Genetics. 2019 Feb;211(2):495-502. doi: 10.1534/genetics.118.301595. Epub 2018 Dec 27.


R/qtl2 is an interactive software environment for mapping quantitative trait loci (QTL) in experimental populations. The R/qtl2 software expands the scope of the widely used R/qtl software package to include multiparent populations derived from more than two founder strains, such as the Collaborative Cross and Diversity Outbred mice, heterogeneous stocks, and MAGIC plant populations. R/qtl2 is designed to handle modern high-density genotyping data and high-dimensional molecular phenotypes, including gene expression and proteomics. R/qtl2 includes the ability to perform genome scans using a linear mixed model to account for population structure, and also includes features to impute SNPs based on founder strain genomes and to carry out association mapping. The R/qtl2 software provides all of the basic features needed for QTL mapping, including graphical displays and summary reports, and it can be extended through the creation of add-on packages. R/qtl2, which is free and open source software written in the R and C++ programming languages, comes with a test framework.

Keywords: Collaborative Cross; Diversity Outbred mice; MAGIC; MPP; Multiparent Advanced Generation Inter-Cross (MAGIC); QTL; heterogeneous stock; multiparent populations; software.

Publication types

  • Research Support, N.I.H., Extramural

MeSH terms

  • Animals
  • Chromosome Mapping / methods*
  • Genome-Wide Association Study / methods*
  • Genotyping Techniques / methods*
  • Mice
  • Quantitative Trait Loci*
  • Software*