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, https://www.genetics.org/content/genetics/211/2/495.full.pdf, https://doi.org/10.1534/genetics.118.301595.

Corresponding BibTeX entry:

  @Article{Broman2018,
    title = {R/qtl2: software for mapping quantitative trait loci with
      high-dimensional data and multi-parent populations.},
    author = {Karl W. Broman and Daniel M. Gatti and Petr Simecek and
      Nicholas A. Furlotte and Pjotr Prins and Śaunak Sen and Brian S.
      Yandell and Gary A. Churchill},
    journal = {Genetics},
    doi = {10.1534/genetics.118.301595},
    year = {2018},
    volume = {211},
    pages = {495-502},
    url = {https://doi.org/10.1534/genetics.118.301595},
    eprint =
      {https://www.genetics.org/content/genetics/211/2/495.full.pdf},
  }