BEAR Applications

VEP 96.0-foss-2019a-Perl-5.28.1

There is a newer version of VEP

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.

Accessing VEP 96.0-foss-2019a-Perl-5.28.1

To load the module for VEP 96.0-foss-2019a-Perl-5.28.1 please use this command on the BEAR systems (BlueBEAR, BEARCloud VMs, and CaStLeS VMs):

module load VEP/96.0-foss-2019a-Perl-5.28.1

BEAR Apps Version

2019a

Architectures

EL8-cascadelake — EL8-haswell — Ubuntu20.04-haswell

The listed architectures consist of two part: OS-CPU.

• BlueBEAR: The OS used on BlueBEAR is represented by EL and there are several different processor (CPU) types available on BlueBEAR. More information about the processor types on BlueBEAR is available on the BlueBEAR Job Submission page.
• BEAR and CaStLeS Cloud VMs: These VMs can have one of two OSes. Those with access to a BEAR Cloud or CaStLeS VM should check that the listed architectures for an application include the OS of VM being used. The VMs, irrespective of OS, will use the haswell CPU type.

Extensions

• Archive::Zip 1.67
• Bio::EnsEMBL::XS 2.3.2
• ExtUtils::CppGuess 0.20
• ExtUtils::MakeMaker 7.38
• Set::IntervalTree 0.12
• SUPER 1.20190531
• Test::MockModule 0.171.0

More Information

For more information visit the VEP website.

Dependencies

This version of VEP has a direct dependency on: Bio-DB-BigFile/1.07-foss-2019a-Perl-5.28.1 Bio-DB-HTS/3.01-GCC-8.2.0-2.31.1-Perl-5.28.1 BioPerl/1.7.2-GCCcore-8.2.0-Perl-5.28.1 DBD-mysql/4.050-foss-2019a-Perl-5.28.1 foss/2019a Perl/5.28.1-GCCcore-8.2.0

Other Versions

These versions of VEP are available on the BEAR systems (BlueBEAR, BEARCloud VMs, and CaStLeS VMs). These will be retained in accordance with our Applications Support and Retention Policy.

Last modified on 3rd December 2019