maftools can be cited as:

  Mayakonda A, Lin DC, Assenov Y, Plass C, Koeffler HP. 2018. Maftools:
  efficient and comprehensive analysis of somatic variants in cancer.
  Genome Research. http://dx.doi.org/10.1101/gr.239244.118

A BibTeX entry for LaTeX users is

  @Article{,
    title = {Maftools: efficient and comprehensive analysis of somatic variants in cancer.},
    author = {Anand Mayakonda and Dechen Lin and Yassen Assenov and Christoph Plass and Phillip H Koeffler},
    journal = {Genome Research},
    year = {2018},
    doi = {http://dx.doi.org/10.1101/gr.239244.118},
  }