SnpEff statistics

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Citations per year

Number of citations per year for the bioinformatics software tool SnpEff
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Tool usage distribution map

This map represents all the scientific publications referring to SnpEff per scientific context
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Associated diseases

This word cloud represents SnpEff usage per disease context
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Popular tool citations

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Protocols

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


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Versioning


No version available

Documentation


Maintainer


  • person_outline Douglas M. Ruden

Additional information


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

Publication for SnpEff

SnpEff citations

 (759)
library_books

Copy number variants implicate cardiac function and development pathways in earthquake induced stress cardiomyopathy

2018
Sci Rep
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), Seatt […]

library_books

Parental haplotype specific single cell transcriptomics reveal incomplete epigenetic reprogramming in human female germ cells

2018
Nat Commun
PMCID: 5951918
PMID: 29760424
DOI: 10.1038/s41467-018-04215-7

[…] recalibrator steps on the SNPs and indels. The resulting VCF files were then filtered for high-quality heterozygous SNPs in the non-parental samples. The final list of variants as annotated using the SnpEff tool (version 4.0), setting the source genome to ‘hg19‘.Construction of parental genomes: High quality (PASS filter tag), heterozygous SNPs from each fetus and high quality homozygous SNPs of t […]

library_books

A case report of heterozygous TINF2 gene mutation associated with pulmonary fibrosis in a patient with dyskeratosis congenita

2018
PMCID: 5959423
PMID: 29742735
DOI: 10.1097/MD.0000000000010724

[…] chment 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 variants […]

library_books

A genome wide survey of mutations in the Jurkat cell line

2018
BMC Genomics
PMCID: 5941560
PMID: 29739316
DOI: 10.1186/s12864-018-4718-6

[…] kat were also found in ClinVar, but the annotations do not contain gene information and are generally less informative (Additional files  and ). 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 a […]

library_books

Comparative Population Genomics Analysis of the Mammalian Fungal Pathogen Pneumocystis

2018
MBio
PMCID: 5941068
PMID: 29739910
DOI: 10.1128/mBio.00381-18

[…] es: -window 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 (). […]

library_books

Ancient DNA study reveals HLA susceptibility locus for leprosy in medieval Europeans

2018
Nat Commun
PMCID: 5931558
PMID: 29717136
DOI: 10.1038/s41467-018-03857-x

[…] al realignment, $REALIGNED is the output from the local realignment and $VFC is the output variant call set in VCF format.To annotate an estimated effect of identified genomic variation, the software SnpEff v4.2 was applied. We used the default parameters and the following command line:java -jar snpEff.jar eff $GFF $VCFwhere $GFF is a previously set up database based on a GFF file and $VCF is the […]


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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.