SOFT : Ensembl-VEP
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Site du soft: https://github.com/Ensembl/ensembl-vep
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LICENSE:
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Apache-2.0 license 

See software documentation for more informations.

Location: /usr/local/bioinfo/src/Ensembl-VEP
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Load binaries and environment:
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-> Version v106.1

module load bioinfo/Ensembl-VEP/106.1

-> Version v108.2

module load bioinfo/Ensembl-VEP/108.2

-> Version v110.1

module load bioinfo/Ensembl-VEP/110.1

-> Version v111.0

module load bioinfo/Ensembl-VEP/111.0

Vep plugin path: /usr/local/bioinfo/src/Ensembl-VEP/ensembl-vep-v111.0/plugins

A ajouter dans la ligne de commande: 
--dir_plugins /usr/local/bioinfo/src/Ensembl-VEP/ensembl-vep-v111.0/plugins 


Warning! --database option will fail due to new firewall configuration to avoid massive request on the remote Ensembl mysql server, 
which ended up with genotoul-bioinfo IPs banned from Ensembl access.
Use instead: --cache --dircache=/usr/local/bioinfo/src/Ensembl-VEP/CACHEDIR --offline 
only annotated genomes present in this folder can be used with --species --assembly or --cache_version
For instance CACHEDIR/homo_sapiens/106_GRCh38/ means :
- species is homo_sapiens
- assembly version for it is GRCh38 
- and Ensembl annotation version used is 106

If you plan to use option --hgvs, add --fasta PATH_TO_GENOME_FASTA (or its gbzip compressed version)
You must have write permission on FASTA file's folder, because indexes will be built the first time you'll use it.

If you need new species/assembly/annotation versions, you can do it by yourself:
http://www.ensembl.org/info/docs/tools/vep/script/vep_cache.html#pre
and change the --dircache to a place you own ... of course.



Example directory for use on cluster:
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/usr/local/bioinfo/src/Ensembl-VEP/example_on_cluster

To submit: sbatch test_ensembl-vep-v110.1.sh 

See software documentation and our FAQ (http://bioinfo.genotoul.fr/index.php/faq/) for more informations.