[ensembl-dev] what are all possible feature_types and variant_feature_types for VEP plugins?

[Michael Yourshaw]

I’m having a bit of trouble capturing all possible features and feature types in plugins where I want to add an annotation to every line of output, for example allele frequencies from an external database.

My current list is
feature_types: ['Transcript', 'RegulatoryFeature', 'MotifFeature', 'Intergenic', 'Gene', 'Exon’] (gene and Exon are produced by some structural variations)
variant_feature_types: ['VariationFeature', 'StructuralVariationFeature’]

If I want to be sure of getting everything, what should I use?

It might be a good enhancement to allow ‘*’ or ‘All’ for these functions so a plugin need not be concerned with knowing all the possibilities when it doesn’t care what they are.


ॐ

Michael Yourshaw
UCLA Geffen School of Medicine
Department of Human Genetics, Nelson Lab
695 Charles E Young Drive S
Gonda 5554
Los Angeles CA 90095-8348 USA
myourshaw at ucla.edu
970.691.8299

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