Entering edit mode
I saw the following messages
Package 'ensemblVEP' is deprecated and will be removed from
Bioconductor version 3.20; Functionality has been moved to
VariantAnnotation
I am trying to migrate to the new package, but upon reading the documents of VariantAnnotation I don't see any function similar to the ensemblVEP() function. The best I can get is vep_by_region() that has only three arguments.
Am I missing something. Now stuck with the old version.
What aspect of ensemblVEP are you looking for? The vignette
https://bioconductor.org/packages/release/bioc/vignettes/VariantAnnotation/inst/doc/ensemblVEP.html
illustrates several aspects of usage of the REST API. Interfacing to VEP through the perl utility would be possible for a community developer who wished to restore the ensemblVEP package functionality, but the core developers of the project will not undertake this at this time.
Please file issues concerning VariantAnnotation at https://github.com/Bioconductor/VariantAnnotation/issues; some open issues are present but the main package creator has left the project.