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
- Documentation: http://snpeff.sourceforge.net/SnpEff_manual.html
Maintainer
- person_outline Douglas M. Ruden <>
Additional information
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
- Documentation: http://snpeff.sourceforge.net/SnpEff_manual.html
Maintainer
- person_outline Douglas M. Ruden <>
Additional information
Publication for SnpEff
SnpEff citations
(37)The Pattern and Distribution of Induced Mutations in J. curcas Using Reduced Representation Sequencing
[…] (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: […]
[…] (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 […]
[…] 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 […]
[…] 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, […]
[…] 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 review
