[ensembl-dev] new VEP REST endpoint

[Michael Heuer]

On Wed, Dec 10, 2014 at 12:05 PM, Michael Heuer <heuermh at gmail.com> wrote:

> 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".
>

I'm sorry, I might have this backward; COSMIC defines this variation as

Mutation Id: COSM476 AA Mutation: p.V600E ( Substitution - Missense ) CDS
Mutation: c.1799T>A ( Substitution )
http://cancer.sanger.ac.uk/cosmic/mutation/overview?id=476

codons/amino_acids and HGVS appear correct but allele_string and
variant_allele have it flipped, shouldn't allele_string be "T/A",
variant_allele "A" and reference_allele "T"?

   "id": "COSM476",
   "allele_string": "A/T",

   "transcript_consequences": [
      {
        "variant_allele": "T",

        "codons": "gTg/gAg",
        "hgvsc": "ENST00000479537.3:c.83T>A",

        "amino_acids": "V/E",
        "hgvsp": "ENSP00000418033.1:p.Val28Glu",
  }

   michael
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