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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
- 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
(759)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), Seatt […]
Parental haplotype specific single cell transcriptomics reveal incomplete epigenetic reprogramming in human female germ cells
[…] 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 […]
A case report of heterozygous TINF2 gene mutation associated with pulmonary fibrosis in a patient with dyskeratosis congenita
[…] 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 […]
A genome wide survey of mutations in the Jurkat cell line
[…] 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 […]
Comparative Population Genomics Analysis of the Mammalian Fungal Pathogen Pneumocystis
[…] 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 (). […]
Ancient DNA study reveals HLA susceptibility locus for leprosy in medieval Europeans
[…] 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 […]
SnpEff review
