ensemblVEP deprecation and how to reproduce
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kmzhou4 • 0
@091bf034
Last seen 4 weeks ago
United States

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.

VariantAnnotation • 246 views
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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.

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