Global InformationSnpEff information
 | This article contains content that is written like an advertisement. (March 2020) |
| Original author(s) | Pablo Cingolani |
|---|---|
| Initial release | 2012 |
| Stable release | 5.2
/ September 29, 2023 |
| Repository | github |
| Written in | Java |
| License | MIT |
| Website | pcingola |
SnpEff is an open source tool that performs annotation on variants and predicts their effects on genes by using an interval forest approach. This program takes pre-determined variants listed in a data file that contains the nucleotide change and its position and predicts if the variants are deleterious. This program was first created by Pablo Cingolani to predict effects of single nucleotide polymorphisms (SNPs) in Drosophila,[1] and is now widely used at many universities such as Harvard University, UC Berkeley, Stanford University etc.[2] SnpEff has been used for various applications[3][4][5] – from personalized medicine at Stanford University,[6] to profiling bacteria.[7] This annotation and prediction software can be compared to ANNOVAR and Variant Effect Predictor, but each use different nomenclatures [8][9]
- ^ "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 [PubMed - in process]
- ^ "SnpEff." SnpEff. N.p., n.d. Web. 28 Feb. 2017. <http://snpeff.sourceforge.net/SnpEff.html#who>.
- ^ Medina, Ignacio, et al. "VARIANT: Command Line, Web service and Web interface for fast and accurate functional characterization of variants found by Next-Generation Sequencing." Nucleic Acids Research 40.W1 (2012): W54-W58.
- ^ Kim, Yun Joong, et al. "Neuroimaging studies and whole exome sequencing of PLA2G6-associated neurodegeneration in a family with intrafamilial phenotypic heterogeneity." Parkinsonism & related disorders 21.4 (2015): 402-406.
- ^ Reddy, Mettu M., and Kandasamy Ulaganathan. "Draft genome sequence of Oryza sativa elite indica cultivar RP Bio-226." Frontiers in plant science 6 (2015).
- ^ Dewey, Frederick E., et al. "Distribution and clinical impact of functional variants in 50,726 whole-exome sequences from the DiscovEHR study." Science 354.6319 (2016): aaf6814.
- ^ Medvedeva, E. S., et al. "Genomic and proteomic profiles of Acholeplasma laidlawii strains differing in sensitivity to ciprofloxacin." Doklady Biochemistry and Biophysics. Vol. 466. No. 1. Pleiades Publishing, 2016.
- ^ Wang K, Li M, Hakonarson H. ANNOVAR: Functional annotation of genetic variants from next-generation sequencing data Nucleic Acids Research, 38:e164, 2010
- ^ "Variant Effect Predictor." Variant Effect Predictor. EMBL-EBI, Dec. 2016. Web. 28 Feb. 2017. <http://uswest.ensembl.org/info/docs/tools/vep/index.html>.