Document Type

Article

Publication Date

2-1-2019

Keywords

JMG

JAX Source

Genetics 2019 Feb; 211(2):495-502

Volume

211

Issue

2

First Page

495

Last Page

502

ISSN

1943-2631

PMID

30591514

DOI

https://doi.org/10.1534/genetics.118.301595

Grant

GM070683

Abstract

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.

Comments

This article is distributed under the terms of the Creative Commons Attribution-NonCommercial 4.0 License.

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