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SnpEff

Description

snpeff website

SnpEff is a variant annotation and effect prediction tool. It annotates and predicts the effects of variants on genes (such as amino acid changes).

Typical usage :

Input: The inputs are predicted variants (SNPs, insertions, deletions and MNPs). The input file is usually obtained as a result of a sequencing experiment, and it is usually in variant call format (VCF).

Output: SnpEff analyzes the input variants. It annotates the variants and calculates the effects they produce on known genes (e.g. amino acid changes). A list of effects and annotations that SnpEff can calculate can be found here.

Environment Modules

Run module spider snpeff to find out what environment modules are available for this application.

Environment Variables

  • HPC_SNPEFF_DIR - installation directory
  • HPC_SNPEFF_BIN - executable directory
  • HPC_SNPEFF_CONF - configuration file directory
  • HPC_SNPEFF_EX - examples directory

Additional Usage Information

In SnpEff-4.x series the upstream project provides a shell script snpEff, which can be used to run the program without calling java directly.

For snpeff/3.3h we provided a snpeff wrapper that made running snpeff easier.

For example, the below command: 

java -Xmx2g -jar $HPC_SNPEFF_DIR/jar/snpEff.jar download -c $HPC_SNPEFF_CONF/snpEff.config -v athalianaTair10
could be run simply as: 
snpeff download -v athalianaTair10
To override the default 2g java memory setting use the following command on the command-line or in a job script: 
export _JAVA_OPTIONS="-Xmx4g"

Reference Databases

Note

We provide a full mirror of snpeff/4.2 reference databases released by the upstream project, so please do not request addition of a new reference database unless you need a custom database built from your data. Please provide a fasta file and an annotation file for building the custom database.

Citation

If you publish research that uses snpeff you have to cite it as follows:

SnpEff:

"A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff: SNPs in the genome of Drosophila melanogaster strain w1118; iso-2; iso-3.", Cingolani P, Platts A, Wang le L, Coon M, Nguyen T, Wang L, Land SJ, Lu X, Ruden DM. Fly (Austin). 2012 Apr-Jun;6(2):80-92. PMID: 22728672 https://doi.org/10.4161/fly.19695

SnpSift:

"Using Drosophila melanogaster as a model for genotoxic chemical mutational studies with a new program, SnpSift", Cingolani, P., et. al., Frontiers in Genetics, 3, 2012. https://doi.org/10.3389/fgene.2012.00035

Categories

biology, annotation