Installing and Configuring SnpEff

MiModD can use SnpEff (v3.3 through 4.0) during variant annotation.

Warning

Version 0.1.5.1 of MiModD supports SnpEff v4.0, but NOT v4.1, which introduced a change in SnpEff variant annotation. We are planning to support v4.1 with the next release of MiModD.

Installation of SnpEff is optional (though we recommend making use of this option) and can be done at any time, i.e. you do not have to have SnpEff to install MiModD.

additional requirement

SnpEff is written in and, thus, requires Java, which you may need to install separately.

You can download SnpEff from http://snpeff.sourceforge.net/.

To install it, simply unpack the downloaded archive to a newly created snpEff folder in your home directory or, if you prefer a different installation directory, read the instructions at http://snpeff.sourceforge.net/download.html#install.

To activate SnpEff-dependent functionality of MiModD, you will have to configure the SNPEFF_PATH parameter in MiModD (see Configuring MiModD for your system).

MiModD does (intentionally) NOT support SnpEff’s database on-demand download feature. This means that you will have to install SnpEff genome files manually before you can use them.

The procedure to do so is explained here in the SnpEff Documentation.

One way to learn about which SnpEff genome files are available for download suggested by the manual is through the command line via (assuming you are running this from the directory you installed SnpEff to):

java -jar snpEff.jar databases

but since this will list all available downloads (> 20000 according to the manual), we recommend using:

java -jar snpEff.jar databases | grep "your search term for your organism"

For example, at the time of writing and for the installed version of SnpEff, the output of:

java -jar snpEff.jar databases | grep "elegans"

, which may be used to search for available genome files for C. elegans, was (with line-wrapping removed):

GCA_000162475.1.18    Granulicatella_elegans_atcc_700633          http://downloads.sourceforge.net/project/snpeff/databases/v3_6/snpEff_v3_6_GCA_000162475.1.18.zip
GCA_000162475.1.21    Granulicatella_elegans_atcc_700633          http://downloads.sourceforge.net/project/snpeff/databases/v3_6/snpEff_v3_6_GCA_000162475.1.21.zip
WBcel215.68           Caenorhabditis_elegans                      http://downloads.sourceforge.net/project/snpeff/databases/v3_6/snpEff_v3_6_WBcel215.68.zip
WBcel215.69           Caenorhabditis_elegans                      http://downloads.sourceforge.net/project/snpeff/databases/v3_6/snpEff_v3_6_WBcel215.69.zip
WBcel215.70           Caenorhabditis_elegans                      http://downloads.sourceforge.net/project/snpeff/databases/v3_6/snpEff_v3_6_WBcel215.70.zip
WBcel235.18           Caenorhabditis_elegans                      http://downloads.sourceforge.net/project/snpeff/databases/v3_6/snpEff_v3_6_WBcel235.18.zip
WBcel235.21           Caenorhabditis_elegans                      http://downloads.sourceforge.net/project/snpeff/databases/v3_6/snpEff_v3_6_WBcel235.21.zip
WBcel235.71           Caenorhabditis_elegans                      http://downloads.sourceforge.net/project/snpeff/databases/v3_6/snpEff_v3_6_WBcel235.71.zip
WBcel235.72           Caenorhabditis_elegans                      http://downloads.sourceforge.net/project/snpeff/databases/v3_6/snpEff_v3_6_WBcel235.72.zip
WBcel235.73           Caenorhabditis_elegans                      http://downloads.sourceforge.net/project/snpeff/databases/v3_6/snpEff_v3_6_WBcel235.73.zip
WBcel235.74           Caenorhabditis_elegans                      http://downloads.sourceforge.net/project/snpeff/databases/v3_6/snpEff_v3_6_WBcel235.74.zip
WBcel235.75           Caenorhabditis_elegans                OK    http://downloads.sourceforge.net/project/snpeff/databases/v3_6/snpEff_v3_6_WBcel235.75.zip
WS220.64              Caenorhabditis_elegans                      http://downloads.sourceforge.net/project/snpeff/databases/v3_6/snpEff_v3_6_WS220.64.zip
WS220.65              Caenorhabditis_elegans                      http://downloads.sourceforge.net/project/snpeff/databases/v3_6/snpEff_v3_6_WS220.65.zip
WS220.66              Caenorhabditis_elegans                      http://downloads.sourceforge.net/project/snpeff/databases/v3_6/snpEff_v3_6_WS220.66.zip
WS241                 C. elegans                                  http://downloads.sourceforge.net/project/snpeff/databases/v3_6/snpEff_v3_6_WS241.zip

Then, following the documentation, to install the latest genome version file you could either run:

java -jar snpEff.jar download WS241

or visit the download link for this version and extract the downloaded archive in the data subfolder of your SnpEff installation.