SnpEff pipeline

SnpEff specifications

Information


Unique identifier OMICS_00186
Name SnpEff
Interface Web user interface
Restrictions to use None
Input data Predicted variants (SNPs, insertions, deletions, MNPs)
Input format VCF
Output data SnpEff analyzes the input variants. It annotates the variants and calculates the effects they produce on known genes (e.g. amino acid changes).
Computer skills Basic
Stability Stable
Maintained Yes

Taxon


  • Animals
    • Homo sapiens

Subtool


  • ClinEff

Documentation


Maintainer


  • person_outline Douglas M. Ruden <>

Additional information


http://www.dnaminer.com/clineff.html

Information


Unique identifier OMICS_00186
Name SnpEff
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input data Predicted variants (SNPs, insertions, deletions, MNPs)
Input format VCF
Output data SnpEff analyzes the input variants. It annotates the variants and calculates the effects they produce on known genes (e.g. amino acid changes).
Operating system Unix/Linux
Programming languages Java
License GNU Lesser General Public License version 3.0
Computer skills Advanced
Version 4.3
Stability Stable
Source code URL http://snpeff.sourceforge.net/download.html#source
Maintained Yes

Taxon


  • Animals
    • Homo sapiens

Subtool


  • ClinEff

Download


Versioning


Add your version

Documentation


Maintainer


  • person_outline Douglas M. Ruden <>

Additional information


http://www.dnaminer.com/clineff.html

Publication for SnpEff

SnpEff citations

 (37)
2018
PMCID: 5944264

[…] (fwf, p 23836), ffg and bioplant r&d., http://www.kazusa.or.jp/jatropha/ , http://bio-bwa.sourceforge.net/ , ftp://ftp.kazusa.or.jp/pub/jatropha/ , https://github.com/ekg/freebayes , http://snpeff.sourceforge.net/ , http://snpeff.sourceforge.net , ftp://ftp.kazusa.or.jp/pub/jatropha/ , the supplementary material for this article can be found online at: […]

2018
PMCID: 5887293

[…] (vcf) from 1,135 natural inbred lines curated by the 1001 genomes project (alonso-blanco et al. 2016). snps in protein-coding genes were annotated as synonymous or nonsynonymous polymorphisms using snpeff (cingolani et al. 2012)., the b. rapa snps were called from the transcriptomes of 126 accessions (qi et al. 2017), and also annotated with snpeff. low quality snps were removed with vcffilter […]

2018
PMCID: 5790234

[…] as burn-in. figtree (http://tree.bio.ed.ac.uk/software/figtree/) was used to visualize the maximum clade credibility (mcc) tree., the vcf files for the ch4, sm1, and cm1 samples were analyzed using snpeff v4.3 [50]. the program was run using default parameters, except the parameter for reporting snps that are located upstream or downstream of protein-coding genes was set to 100 bases., buccal […]

2018
PMCID: 5927534

[…] the mm9 version of the mouse reference genome using the star aligner. the gatk pipeline was used to call variants from the aligned data to generate a vcf file, which was subsequently annotated using snpeff and filtered for trp53 using snpsift., female c57 bl/6 (jackson labs, bar harbor, ma), scid-beige (jackson labs, bar harbor, ma), oti (b6.129s6-rag2tm1fwa-tg(tcratcrb)1100mjb; jackson labs, […]

2017
PMCID: 5725591

[…] the processes of response to stress, cell death, and protein modification were significantly over-represented (figure s2). the impact of the detected snvs on the genes was classified according to snpeff ver. 3.0 and is shown in table 2. snvs having a “high” impact included missense mutations or nonsense ones, such as the loss of the start or stop codon, the generation of a premature stop […]

SnpEff institution(s)
Supported by a Michigan Core Technology grant from the State of Michigan's 21st Century Fund Program to the Wayne State University Applied Genomics Technology Center, the Environmental Health Sciences Center in Molecular and Cellular Toxicology with Human Applications Grant P30 ES06639 at Wayne State University, NIH R01 grants (ES012933) and DK071073.

SnpEff review

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Arup Ghosh

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Web
Really easy to use variant annotation tools compatible with multiple variant calling software outputs. This tool gives the freedom to build custom annotation files and direct import from NCBI GeneBank.