SnpEff

Description

snpeff website  

SnpEff

Genetic variant annotation and effect prediction toolbox. It annotates and predicts the effects of variants on genes (such as amino acid changes).

Features

• Supports over 8,500 genomes.
• Cancer variants analysis
• GATK compatibile (-o gatk)
• HGSV notations support (clinical)

SnpSift

SnpSift helps filtering and manipulating genomic annotated files (VCF). Once you annotated your files using SnpEff, you can use SnpSift to help you filter large genomic datasets in order to find the most significant variants

Required Modules

Serial

• snpeff

System Variables

• HPC_{{#uppercase:snpeff}}_DIR - main installation directory
• HPC_{{#uppercase:snpeff}}_BIN - directory with executable scripts
• HPC_{{#uppercase:snpeff}}_CONF - directory with the default configuration file.

Additional Information

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

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"

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.

Note: as of March 21st, 2016 we have a full mirror of snpeff/4.2 reference databases released by the upstream project, so please do not request addition of new reference databases unless you provide a set of custom fasta and annotation files for building a 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 [PubMed - in process]

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.

Reference Databases

See the installed database lists for

• SnpEff-4.1
• SnpEff-4.2