[ensembl-dev] annotate variants on refseq transcripts through rest api ?

[Will McLaren]

Hi Caleb,

You just need to add a couple of parameters to the standard VEP REST
request:

1) refseq=1 - tells VEP to use RefSeq transcripts instead of Ensembl. You
may request both instead with merged=1

2) numbers=1 - tells VEP to report exon and intron numbers

Here's an example, the same parameters can be used on any vep/ endpoint:

https://rest.ensembl.org/vep/human/id/rs699?content-type=application/json&refseq=1&numbers=1

Regards

Will McLaren
Ensembl Variation

On 5 October 2016 at 17:21, Caleb Davis <caldavis at gmail.com> wrote:

> Hi dev-ensembl,
>
> I would like to annotate intron numbers with respect to refseq
> transcripts for genomic changes  through the rest api, but I can't figure
> out how. It looks like I can do what I want through the command line VEP
> script using --refseq, but I would prefer to use the API if at all
> possible. Please advise.
>
> Many thanks, --Caleb
>
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