R/qtl2 (aka qtl2) is a reimplementation of the QTL analysis software R/qtl, to better handle high-dimensional data and complex cross designs.

Discussion group

For discussion/questions about R/qtl2, join the rqtl2-disc google group. Or join rqtl-announce for announcements about R/qtl and R/qtl2. (We’ll try to keep the original rqtl-disc group for the discussion/questions about the original R/qtl only.)

Installation

Install R/qtl2 from CRAN:

install.packages("qtl2")

The latest release of R/qtl2 is 0.22-11 (2020-07-09).

Documentation

• user guide
• categorized list of functions in R/qtl2
• input file formats (also see the sample data files and the qtl2data repository)
• preparing DO mouse data for R/qtl2
• genotype diagnostics for diversity outbred mice
• differences between R/qtl and R/qtl2
• developer guide
• HMM benchmarks
• Tutorial on R/qtl2 by Susan McClatchy and Dan Gatti

Citation

To cite R/qtl2 in publications, use:

Broman KW, Gatti DM, Simecek P, Furlotte NA, Prins P, Sen Ś, Yandell BS, Churchill GA (2018) R/qtl2: software for mapping quantitative trait loci with high-dimensional data and multi-parent populations. Genetics 211:495-502 doi:10.1534/genetics.118.301595

License

Licensed under GPL-3.

Sources on github:

• The source for R/qtl2
• The source for R/qtl2convert and R/qtl2fst
• The source for this website