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The SnpEff configuration file is essential for specifying key run parameters, including (most importantly), the location of the databases to be used for your analysis.  For your convenience, a configuration file template has been provided for your use in the following common directory:

 

/
mnt
opt/
research
software/
common-data/Bio/SnpEff/
SnpEff/4.2/snpEff.config

 

To use SnpEff, you first need to copy this file to your working directory, and make any necessary changes desired for your analysis.  Note that the configuration parameter "data_dir" (the database location) defaults to the following path in your home directory space:

 

data_dir = ~/snpEff/data/

 

You may leave this as-is, providing you actually place your databases in this path.  Otherwise, you will need to update it to match the correct location.

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The current list of pre-built databases available for SnpEff can be obtained by using the following:

 

module load SnpEff
java -jar $SNPEFF/snpEff.jar databases

 

For your convenience, a list has been created and is available for your inspection in the common directory path:

 

/mnt/research/common-data/Bio/SnpEff/supported_dbs

 

Grep'ing on that file is probably the easiest method of finding out if your genome is supported.

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However, the recommended method of obtaining the most recent pre-built databases is to use the SnpEff command itself.  For example:

 

cd ~/snpEff/data
module load SnpEff
java -jar $SNPEFF/snpEff.jar download GRCh37.69

 

Using the above would place a copy of the Human Genome in the directory ~/snpEff/data.  

Note that grep'ing on the "supported_dbs" file yields the following:

 

cat /mnt/research/common-data/Bio/SnpEff/supported_dbs | grep GRCh37.69
 
GRCh37.69                                                       Homo_sapiens                                                                http://sourceforge.net/projects/snpeff/files/databases/v3.3/snpEff_v3.3_Homo_sapiens.zip

 

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Pre-built SnpEff databases are segregated by version. For example, if the version of SnpEff you're using is v. 3.3, you will want to download the database from the v. 3.3 subdirectory of the SnpEff website. Using the "download" command ensures you will get the correct database for your version.

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Once you have made the necessary modifications to your configuration file, and downloaded your desired databases, you are ready to run SnpEff.  As part of executing the SnpEff command, make sure to specify the location of the configuration file you wish to use for the run. 

For example:

 

module load SnpEff
java -jar $SNPEFF/snpEff.jar -c /path/to/configuration/file/snpEff.config <args>

 

More information

For more information on using SnpEff, please refer to the following documentation:

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