[ensembl-dev] new VEP REST endpoint

[Michael Heuer]

Hello,

I'm finally getting the chance to update some code that depends on the VEP
REST endpoint from the beta version to the current production version and
have a few questions.  Looking specifically at this example

http://rest.ensembl.org/vep/human/id/COSM476?content-type=application/json

Under transcript_consequences in this example somatic is "1,1,1".  What is
this supposed to represent?  There are three colocated_variants, so I
assume this is referring to that.

Under transcript_consequences allele_string="A/T" is now represented as
variant_allele="T".  It would be useful to have a similar
reference_allele="A".

Then in this table there are a few cases documented where VEP isn't using
the correct SO term:

http://gemini.readthedocs.org/en/latest/content/functional_annotation.html#standardizing-impact-definitions-for-gemini

Have these been addressed?

Thank you,

   michael
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