VEP

VEP is a software module available on Comet.

To access VEP on Comet, run module load VEP. This will load the default version of VEP.

An overview of the module information is shown below (module -r spider ^VEP$):

VEP: VEP/113.3-GCC-13.3.0
    Description:
      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. Includes EnsEMBL-XS, which provides pre-compiled
      replacements for frequently used routines in VEP.

    This module can be loaded directly: module load VEP/113.3-GCC-13.3.0

    This module provides the following extensions:

       Bio::EnsEMBL::XS/2.3.2 (E)

    Help:
      
      Description
      ===========
      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.
       Includes EnsEMBL-XS, which provides pre-compiled replacements for frequently
       used routines in VEP.
      
      More information
      ================
       - Homepage: https://www.ensembl.org/info/docs/tools/vep
      
      Included extensions
      ===================
      Bio::EnsEMBL::XS-2.3.2

If there are multiple versions of VEP listed, then you can load a specific version as follows:

$ module load VEP/version_string

You can find the most up to date information whilst logged on to Comet by running module -r spider ^VEP$.

The module VEP has the following embedded help text (module help VEP):

Description
===========
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.
 Includes EnsEMBL-XS, which provides pre-compiled replacements for frequently
 used routines in VEP.

More information
================
 - Homepage: https://www.ensembl.org/info/docs/tools/vep

Included extensions
===================
Bio::EnsEMBL::XS-2.3.2

The default version of the module VEP has the following dependencies:

• GCC/13.3.0
• Perl/5.38.2-GCCcore-13.3.0
• Archive-Zip/1.68-GCCcore-13.3.0
• DBD-mysql/4.051-GCC-13.3.0
• BioPerl/1.7.8-GCCcore-13.3.0
• Bio-DB-HTS/3.01-GCC-13.3.0
• Compress-Raw-Zlib/2.213-GCCcore-13.3.0

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