[ensembl-dev] variant allele of hgvsc on '-' strand using POST vs GET vep/human/region

[Will McLaren]

Hi Caleb,

Your input to the POST endpoint indicates your variant is on the reverse
strand; the "-" in the 5th column tells VEP this. Remove this or replace
with "+" and the answers match OK. See [1] for details.

Your HGVS input to the GET endpoint is implicitly on the forward strand.

Regards

Will McLaren
Ensembl Variation

[1] : http://www.ensembl.org/info/docs/tools/vep/vep_formats.html#input

On 11 July 2016 at 16:04, Caleb Davis <caldavis at gmail.com> wrote:

> Hi dev-ensemble,
>
> I'm a happy user of your code and services. Thank you for all you do.
>
> I noticed a consistent difference between POST and GET commands at the
> vep/human/region endpoint of the v84 API (GRCh37). Specifically, the
> variant allele differs for transcripts on the '-' strand.
>
> e.g. 17 41240915 41240915 A/G - (vep default).
>
> Using POST [1] hgvsc is, e.g. ENST00000346315.3:c.4185+2046T>G (notice
> T>G; not reverse complemented)
>
> Using GET [2] hgvsc is, e.g. ENST00000346315.3:c.4185+2046T>C (T>C;
> reverse complemented)
>
>
> <http://grch37.rest.ensembl.org/vep/human/hgvs/17:g.41240915A%3EG?hgvs&content-type=application/json>Would
> you please take a look? Thanks in advance.
>
> -- Caleb
> Caleb Davis, PhD
> Bioinformatics Scientist
> MolecularMatch, Inc.
> twitter: @cal_dav
>
> [1] curl -X POST -H "content-type: application/json" -H "accept:
> application/json" -H "Cache-Control: no-cache" -H "Postman-Token:
> f224211e-6267-22cf-5a11-65f2cf00631d" -d '{ "variants" : ["17 41240915
> 41240915 A/G -"], "numbers":"1", "hgvs":"1" }' "
> http://grch37.rest.ensembl.org/vep/human/region"
>
> [2]
> http://grch37.rest.ensembl.org/vep/human/hgvs/17:g.41240915A%3EG?hgvs&content-type=application/json
>
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