f you are using SnpEff or SnpSift, please cite our work.

Citing SnpEff:
"A program for annotating and predicting the effects of single
nucleotide polymorphisms, SnpEff: SNPs in the genome of Drosophila
melanogaster strain w1118; iso-2; iso-3.", Cingolani P, Platts A, Wang
le L, Coon M, Nguyen T, Wang L, Land SJ, Lu X, Ruden DM. Fly (Austin).
2012 Apr-Jun;6(2):80-92. PMID: 22728672

You can find the paper here:
http://snpeff.sourceforge.net/SnpEff_paper.pdf

BibTex entry:

@article{cingolani2012program,
  title={A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff: SNPs in the genome of Drosophila melanogaster strain w1118; iso-2; iso-3},
  author={Cingolani, P. and Platts, A. and Coon, M. and Nguyen, T. and Wang, L. and Land, S.J. and Lu, X. and Ruden, D.M.},
  journal={Fly},
  volume={6},
  number={2},
  pages={80-92},
  year={2012}
}