{"id":559,"date":"2015-06-02T17:25:23","date_gmt":"2015-06-02T17:25:23","guid":{"rendered":"http:\/\/ri.itservices.manchester.ac.uk\/icsf\/?page_id=559"},"modified":"2015-06-02T17:42:48","modified_gmt":"2015-06-02T17:42:48","slug":"ensembl","status":"publish","type":"page","link":"https:\/\/ri.itservices.manchester.ac.uk\/icsf\/software\/applications\/ensembl\/","title":{"rendered":"Ensembl Tools"},"content":{"rendered":"

Overview<\/h2>\n

Ensembl<\/a> provides a Variant Effect Predictor script (written in perl) to determine the effect of your variants (SNPs, insertions, deletions, CNVs or structural variants) on genes, transcripts, and protein sequence, as well as regulatory regions.<\/p>\n

Versions 79 and 80 of Ensembl Tools are installed on the iCSF.<\/p>\n

Restrictions on use<\/h2>\n

There are no restrictions on access this software on the iCSF. The software is released under the Apache License<\/a> and all users are required to read and adhere to the license terms.<\/p>\n

Set up procedure<\/h2>\n

To access the software you must first load one<\/em> of the following modulefile:<\/p>\n

\r\nmodule load apps\/binapps\/ensembl\/80\/vep\r\nmodule load apps\/binapps\/ensembl\/79\/vep\r\n<\/pre>\n
This will automatically load the perl 5.20.2 modulefile.<\/p>\n
Running the application<\/h2>\n
Please note that the VEP script will not be able to connect to an external MySQL database. Hence you should use the script in its offline<\/a> mode.<\/p>\n
You will need to download the cache files for offline use. Please see Ensembl Caches and Databases Download<\/a> website for full details. A brief summary is given here:<\/p>\n
First create a directory for the cache files. By default the VEP script assumes the cache files will be in your home directory in a hidden folder named .vep<\/code>. However due to the size of the cache files (approx 4GB each when compressed, more when uncompressed) it is advised you put them in an RDS area<\/a> – e.g., if your group has a shared directory on the Isilon storage or if you have a shortcut in your home directory named data<\/code> pointing at additional Isilon storage for your group. In the example below we assume you have a shortcut named data<\/code> in your home directory. But you can specify any directory name using the flag as indicated below.<\/p>\n
\r\n# Create a directory for your VEP cache files\r\ncd ~\/data\r\nmkdir vep\r\ncd vep\r\n\r\n# Download from the VEP website. For example for version 80, a 4GB (compressed) file:\r\nwget ftp:\/\/ftp.ensembl.org\/pub\/release-80\/variation\/VEP\/homo_sapiens_vep_80_GRCh37.tar.gz\r\n\r\n# Uncompress it (expands to 6.1GB)\r\ntar xzf homo_sapiens_vep_80_GRCh37.tar.gz\r\n\r\n# Optional - remove the original compressed archive\r\nrm homo_sapiens_vep_80_GRCh37.tar.gz\r\n<\/pre>\n
To run the VEP, ensure you have loaded the modulefile above then:<\/p>\n
\r\n# Notice we use the ~\/data\/vep directory created earlier\r\nvariant_effect_predictor.pl --cache --dir_cache ~\/data\/vep --offline  -i input.vcf<\/em> -o output.txt<\/em>\r\n<\/pre>\n
An example input vcf<\/code> file is available by using the filename: <\/p>\n
$ENSEMBL_VEP_DIR\/example_GRCh38.vcf<\/pre>\n
This requires the ensembl modulefile to be loaded before use.<\/p>\n
Further info<\/h2>\n