To cite R/qtl in publications use:

Broman et al. (2003) R/qtl: QTL mapping in experimental crosses. Bioinformatics 19:889-890

Corresponding BibTeX entry:

  @Article{,
    title = {R/qtl: {QTL} mapping in experimental crosses},
    author = {Karl W. Broman and Hao Wu and Saunak Sen and Gary A.
      Churchill},
    journal = {Bioinformatics},
    year = {2003},
    volume = {19},
    pages = {889-890},
  }