SnpEff 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


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

 (122)
2018
PMCID: 5764945
PMID: 29326221
DOI: 10.1128/genomeA.01446-17

[…] the reference genome of a. laidlawii pg-8a (genbank accession number cp000896) and annotation of single nucleotide polymorphisms (snps) were performed using bowtie2 software (14), samtools (15), and snpeff version 3.3 (16). gene prediction and annotation were performed using the ncbi prokaryotic genome annotation pipeline (17)., mutations in the genes associated with the development […]

2018
PMCID: 5776132
PMID: 29387076
DOI: 10.3389/fpls.2017.02269

[…] 2010; depristo et al., 2011). the different snp/indel variants of dj15, koshihikari, nj16, and dongxiang were processed with gatk (mckenna et al., 2010; depristo et al., 2011), and annotated with snpeff (cingolani et al., 2012). candidate genes for salt tolerance in the qtl regions were obtained after filtering out transposons and pseudogenes., the salt-tolerant introgression line dj15 […]

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. 2). this novel mutation […]

2018
PMCID: 5790234
PMID: 29381722
DOI: 10.1371/journal.pntd.0006190

[…] 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: 5826070
PMID: 29515972
DOI: 10.3389/fonc.2018.00032

[…] phd-science without borders)., 1http://dgv.tcag.ca/dgv/app/home., 2http://www.bioinformatics.babraham.ac.uk/projects/fastqc/., 3https://software.broadinstitute.org/gatk/best-practices/., 4http://snpeff.sourceforge.net/., 5www.1000genomes.org/., 6http://evs.gs.washington.edu/evs/., 7http://www.r-project.org/., 8http://david.abcc.ncifcrf.gov/., the supplementary material for this article […]

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

star_border star_border star_border star_border star_border
star star star star star

Arup Ghosh

star_border star_border star_border star_border star_border
star star star star star
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.