To cite package 'sequenza' in publications use:

Favero F, Joshi T, Marquard AM, Birkbak NJ, Krzystanek M, Li Q, Szallasi Z, Eklund AC (2015). “Sequenza: allele-specific copy number and mutation profiles from tumor sequencing data.” Annals of Oncology, 26, 64-70. doi: 10.1093/annonc/mdu479, http://annonc.oxfordjournals.org/content/26/1/64.

Corresponding BibTeX entry:

  @Article{,
    title = {Sequenza: allele-specific copy number and mutation
      profiles from tumor sequencing data},
    author = {Francesco Favero and Tejal Joshi and Andrea M Marquard
      and Nicolai J Birkbak and Marcin Krzystanek and Qiyuan Li and
      Zoltan Szallasi and Aron C Eklund},
    journal = {Annals of Oncology},
    year = {2015},
    volume = {26},
    issue = {1},
    pages = {64-70},
    doi = {10.1093/annonc/mdu479},
    url = {http://annonc.oxfordjournals.org/content/26/1/64},
  }