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

Caleb Davis caldavis at gmail.com
Mon Jul 11 16:04:44 BST 2016


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
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mail.ensembl.org/pipermail/dev_ensembl.org/attachments/20160711/da7488c0/attachment.html>


More information about the Dev mailing list