| The CSF2 has been replaced by the CSF3 - please use that system! This documentation may be out of date. Please read the CSF3 documentation instead. To display this old CSF2 page click here. |
Ensembl
Overview
Ensembl 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.
Version 79 of Ensembl Tools is installed on the CSF.
Restrictions on use
There are no restrictions on access this software on the CSF. The software is released under the Apache License and all users are required to read and adhere to the license terms.
Set up procedure
To access the software you must first load the modulefile:
module load apps/binapps/ensembl/79/vep
This will automatically load the perl 5.20.2 modulefile.
Running the application
Please do not run Ensembl VEP on the login node. Jobs should be submitted to the compute nodes via batch.
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 mode.
Serial batch job submission
Make sure you have the modulefile loaded then create a batch submission script, for example:
#!/bin/bash #$ -S /bin/bash #$ -cwd # Job will run from the current directory #$ -V # Job will inherit current environment settings variant_effect_predictor.pl args
Submit the jobscript using:
qsub scriptname
where scriptname is the name of your jobscript.
Further info
Updates
None.