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

[Will McLaren]

Hi Caleb,

This looks like a bug in our API backend. I'll take a look, but it may be
that we're not able to roll out a fix for this until the next Ensembl
release (in a couple of months' time).

For now it should work fine with HGVS input on anything but RefSeq
identifiers, as well as genomic coordinates/alleles and rsIDs.

Regards

Will

On 5 October 2016 at 17:52, Caleb Davis <caldavis at gmail.com> wrote:

> 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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> >>
>
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