SnpEff statistics

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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


  • Primates
    • 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


  • Primates
    • 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 in pipelines

 (238)
2018
PMCID: 5748942
PMID: 29291727
DOI: 10.1186/s12864-017-4249-6

[…] regions in the genome, we visualized these densities with circos (v0.69) []. we used snpsift (v4.2) [], a vcf-manipulation tool, to extract all the genes contained between the snp-densest regions., snpeff was used to annotate variants of the local strains (v4.2, build 2015–12-05) [], classifying them as synonymous or non-synonymous and obtaining their respective impact according […]

2018
PMCID: 5764945
PMID: 29326221
DOI: 10.1128/genomeA.01446-17

[…] to the reference genome of a. laidlawii pg-8a (genbank accession number cp000896) and annotation of single nucleotide polymorphisms (snps) were performed using bowtie2 software (), samtools (), and snpeff version 3.3 (). gene prediction and annotation were performed using the ncbi prokaryotic genome annotation pipeline ()., mutations in the genes associated with the development of tetracycline […]

2018
PMCID: 5771210
PMID: 29379518
DOI: 10.3389/fpls.2017.02267

[…] the mutation allele]/[number of all reads mapped to the loci]) cutoff was set to 1. snps with large effects on genes (missense, nonsense, splice_site_acceptor, splice_site_donor) predicted by snpeff (cingolani et al., ) were retained as candidate causal mutations. the candidate mutations from two allelic f2 populations were then compared to determine the overlap., to analyze […]

2018
PMCID: 5779785
PMID: 29505016
DOI: 10.1097/MD.0000000000009677

[…] local realignment and base quality recalibration were done by the genome analysis toolkit (gatk ver 3.5). variant calling was performed by gatk haplotypecaller. variants were annotated by snpeff ver 4.2. as a result, 1 heterozygous nonsense mutation, c.1956g>a; p.trp652∗ (reference sequence: nm_001024858.2), was identified in the exon 13 of sptb gene (fig. ). this novel mutation […]

2018
PMCID: 5780301
PMID: 29331171
DOI: 10.1016/j.ymgme.2017.11.003

[…] using bowtie 2 , (2) the duplicates were marked and sorted using picard, (3) variants were called using samtools and bcftools after indel realignment using gatk, (4) transcripts were annotated using snpeff , (5) functional variants were prioritized for rare variants by comparison against the public databases [dbsnp, nhlbi exome sequencing project exome variant server, and exome aggregation […]


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SnpEff in publications

 (867)
PMCID: 5954162
PMID: 29765130
DOI: 10.1038/s41598-018-25827-5

[…] this included de novo assembly at each potential variant locus. variants were annotated and analysed using ingenuity variant analysis (iva) software (qiagen, redwood city, ca, usa), mutationtaster2, snpeff, seattleseq annotation server, and galaxy (via usegalaxy.org). allele frequencies and additional annotations were drawn from 1000 genomes project, nhlbi go exome sequencing project (esp), […]

PMCID: 5959423
PMID: 29742735
DOI: 10.1097/MD.0000000000010724

[…] kit (agilent technologies, california). sequence reads obtained were mapped to the human genome grch37/hg19 assembly using the bwa software and analyzed by the picard-tools-1.118, gatk.v4, and snpeff_v4.1.software.[–] the mean depth of target regions was 141x. variants were annotated using dbsnp142, 1000 genome, esp, clinvar, and our in-house database. finally, candidate pathogenic […]

PMCID: 5944918
PMID: 29746462
DOI: 10.1371/journal.pgen.1007221

[…] genome assemblies and variant calling were the same except that the variant calling for alignment to v1.2 assembly was not limited to marker positions. the detected snps were then annotated with snpeff [] and the p. patens v1.6 genome annotation []. the gbrowser on phytozome.org provided the cross reference of v3 and v1.6 genome annotations, and the v1.6 annotation of all genes located […]

PMCID: 5941560
PMID: 29739316
DOI: 10.1186/s12864-018-4718-6

[…] found in clinvar, but the annotations do not contain gene information and are generally less informative (additional files  and ). table 2 , moving from established to predicted effects, we used snpeff to predict the functional consequences of the gatk-called small variants. snpeff identified 9997 synonymous and 10,984 nonsynonymous mutations. among the nonsynonymous mutations, 252 variants […]

PMCID: 5941068
PMID: 29739910
DOI: 10.1128/mBio.00381-18

[…] 35 -cluster 3 -filtername fs -filter “fs > 30.0” -filtername qd -filter “qd < 2.0.” multisample variant call format (vcf) files were generated using fermikit (). snps were annotated using snpeff (). polymorphic site positions were analyzed using r package adegenet v.2.0.1 ()., we used filtered variants (vcf) to visualize relationships between isolates using principal-component […]


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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.