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

[Caleb Davis]

Thank you, Will. What about for arbitrary NM_* identifiers and hgvs input like:

https://rest.ensembl.org/vep/human/hgvs/NM_003718:c.2897+1G>C?hgvs=1&numbers=1&merged=1&content-type=application/json

I get

{"error":"Could not get a Transcript object for 'NM_003718'"}

Any suggestions? Thanks, --Caleb


> Date: Wed, 5 Oct 2016 17:26:08 +0100
> From: Will McLaren <wm2 at ebi.ac.uk>
> Subject: Re: [ensembl-dev] annotate variants on refseq transcripts
>         through rest api ?
> To: Ensembl developers list <dev at ensembl.org>
> Message-ID:
>         <CAMVEDX3bJ1bCZ4DhHR4Xb1Hr5Jvht0=qTrngVPLEy0AGC63Eew at mail.gmail.com>
> Content-Type: text/plain; charset="utf-8"
>
> 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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