Ensembl-Vep

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  • Homepage: Ensembl Variant Effect Predictor (VEP): determines the effect of your variants (SNPs, insertions, deletions, CNVs or structural variants) on genes, transcripts, and protein sequence, as well as regulatory regions.

Module: Example

[]$ module spider ensembl-vep

-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
  ensembl-vep:
-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
     Versions:
        ensembl-vep/98.3

-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
  For detailed information about a specific "ensembl-vep" module (including how to load the modules) use the module's full name.
  For example:

     $ module spider ensembl-vep/98.3
-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
module load ensembl-vep/98.3

Using:

This application has been installed with:

  • No cache files.
  • No FASTA files.
  • No plugins.

This is because there are 100s of cache and FASTA files and 10s of plugins. Since these are being regularly up[dates and new plugins released, it is too time consuming to track and manage. These will need to be installed locally.

[]$ vep
#----------------------------------#
# ENSEMBL VARIANT EFFECT PREDICTOR #
#----------------------------------#

Versions:
  ensembl              : 98.e98e194
  ensembl-funcgen      : 98.6f9bf7c
  ensembl-io           : 98.052d23b
  ensembl-variation    : 98.7a544e7
  ensembl-vep          : 98.3

Help: dev@ensembl.org , helpdesk@ensembl.org
Twitter: @ensembl

http://www.ensembl.org/info/docs/tools/vep/script/index.html

Usage:
./vep [--cache|--offline|--database] [arguments]

Basic options
=============
--help                 Display this message and quit

-i | --input_file      Input file
-o | --output_file     Output file
--force_overwrite      Force overwriting of output file
--species [species]    Species to use [default: "human"]
                       
--everything           Shortcut switch to turn on commonly used options. See web
                       documentation for details [default: off]                       
--fork [num_forks]     Use forking to improve script runtime

For full option documentation see:
http://www.ensembl.org/info/docs/tools/vep/script/vep_options.html

Dependencies:

  • This software is dependent on the following modules:
    • swset/2018.05
    • gcc/7.3.0
    • Perl Modules:
      • perl-dbi
      • perl-dbd-mysql (and other associated modules)
      • perl-try-tiny
      • The module ensembl-vep/98.3 line will automatically load these modules for you.


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