Annotation with snpEff or VEP

Note

Version support: VEP versions 2.4 through 73 and core SnpEff versions 3.0 through 3.3

Note

Version support would be subsequently updated here, as we test along and add or edit changes available with the latest version of these tools.

Stepwise installation and usage of VEP

Download the Variant Effect Predictor “standalone perl script” from Ensembl. You can choose a specific version of VEP to download here

Example:

Download version 71

Untar the tarball into the current directory

$ tar -zxvf variant_effect_predictor.tar.gz

This will create the variant_effect_predictor directory. Now do the following for install:

$ cd variant_effect_predictor
$ perl INSTALL.pl [options]

By default this would install the API’s, bioperl-1.2.3 and the cache files (in the $HOME/.vep directory).

Manual installation of VEP

For those (e.g mac users) who have a problem installing through this install script, try a manual installation of the API’s, BioPerl-1.2.3 and set all pre-requisites for running VEP (DBI and DBD::mysql modules required). The appropriate pre-build caches should be downloaded for Human to the $HOME/.vep directory and then untar.

You may follow instructions at http://www.ensembl.org/info/docs/api/api_installation.html which provides alternate options for the API installation and additional tips for windows/mac users. It also has information for setting up your environment to run VEP.

Example download of the cache files

$ wget ftp://ftp.ensembl.org/pub/release-73/variation/VEP/homo_sapiens_vep_73.tar.gz

You may change the release date in this example to get the appropriate cache files for your version of VEP that you have installed.

Example

$ wget ftp://ftp.ensembl.org/pub/release-71/variation/VEP/homo_sapiens_vep_71.tar.gz

Cache requires the gzip and zcat utilities. VEP uses zcat to decompress cached files. For systems where zcat may not be installed or may not work, the following option needs to be added along with the --cache option:

--compress "gunzip -c"

Running VEP

You may now run VEP as:

$ perl variant_effect_predictor.pl [OPTIONS]

We recommend running VEP with the following options as currently we support VEP fields specified as below:

$ perl variant_effect_predictor.pl -i example.vcf \
   --cache \
   --terms so \
   --sift b \
   --polyphen b \
   --hgnc \
   --numbers \
   -o output \
   --vcf \
   --fields Consequence,Codons,Amino_acids,Gene,HGNC,Feature,EXON,PolyPhen,SIFT

    N.B. For VEP version 73, replace "--hgnc" with "--symbol" & "HGNC" in --fields to "SYMBOL"

A documentation for the above specified options may be found at http://www.ensembl.org/info/docs/tools/vep/script/vep_options.html

Stepwise installation and usage of SnpEff

Note

Basic Requirements: Java v1.6 or later; at least 2GB of memory

Download the supported versions of SnpEff from http://snpeff.sourceforge.net/download.html

Example:

$ wget http://sourceforge.net/projects/snpeff/files/snpEff_v3_0_core.zip

Note

SnpEff should be installed preferably in snpEff directory in your home directory. Else, you must update the data_dir parameter in your snpEff.config file. For e.g. if the installation of snpEff has been done in ~/src instead of ~/ then change the data_dir parameter in snpEff.config to data_dir = ~/src/snpEff/data/

Unzip the downloaded package.

$ unzip snpEff_v3_0_core.zip

Change to the snpEff directory and download the genome database.

$ cd snpEff_v3_0_core
$ java -jar snpEff.jar download GRCh37.66

Unzip the downloaded genome database. This will create and place the genome in the ‘data’ directory

$ unzip snpEff_v3_0_GRCh37.66.zip

To annotate a vcf using snpEff, use the default options as below:

Note

Memory options for the run may be specified by -Xmx2G (2GB) or Xmx4G (4GB) based on the requirement

$ java -Xmx4G -jar snpEff.jar -i vcf -o vcf GRCh37.66 example.vcf > example_snpeff.vcf

If running from a directory different from the installation directory, the complete path needs to be specified as, e.g.:

$ java -Xmx4G -jar path/to/snpEff/snpEff.jar -c path/to/snpEff/snpEff.config GRCh37.66 path/to/example.vcf > example_snpeff.vcf
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