SnpEff statistics
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
No version available
Documentation
- Documentation: http://snpeff.sourceforge.net/SnpEff_manual.html
Maintainer
- person_outline Douglas M. Ruden
Additional information
Publication for SnpEff
SnpEff citations
(979)Copy number variants implicate cardiac function and development pathways in earthquake induced stress cardiomyopathy
[…] 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), […]
Parental haplotype specific single cell transcriptomics reveal incomplete epigenetic reprogramming in human female germ cells
[…] 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 […]
A case report of heterozygous TINF2 gene mutation associated with pulmonary fibrosis in a patient with dyskeratosis congenita
[…] 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 […]
Conditional genetic screen in Physcomitrella patens reveals a novel microtubule depolymerizing end tracking protein
[…] 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 […]
A genome wide survey of mutations in the Jurkat cell line
[…] 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 […]
Comparative Population Genomics Analysis of the Mammalian Fungal Pathogen Pneumocystis
[…] 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 […]
SnpEff review
