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
- 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
-
Primates
- 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 IN pipelines
(122)[…] 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 […]
[…] 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 […]
[…] 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 […]
[…] 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 […]
[…] 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 review
