Ensembl VEP has been developed for use on Linux systems and we recommend installing on a Linux system for the optimal installation and usage experience. However, we occasionally receive queries about using VEP in the Windows environment – this guide will help you get going if you are using Windows 10.
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Cool stuff the VEP can do: Singularity
The quickest and most flexible way to run Ensembl VEP on large scale variant sets is to install and run it locally. Depending on the use case, the underlying architecture, and the available permissions, installing VEP prerequisites is prone to complications. To aid with this, we have made the VEP available with containers.
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