[ensembl-dev] Mapping genomic coordinates to CDS

[Will McLaren]

Hi Greg,

The VEP endpoints will take genomic coords and give you CDS coordinates
(along with many other things that you may not want!):
http://rest.ensembl.org/documentation/info/vep_region_get

There is also a POST endpoint.

You could also use the local VEP script to do the same with the benefit of
adding speed and being able to customise your output more:

http://www.ensembl.org/info/docs/tools/vep/script/index.html

Regards

Will McLaren
Ensembl Variation

On 5 November 2015 at 16:59, Greg Slodkowicz <gregs at ebi.ac.uk> wrote:

> Dear all,
> I'm working with a large (>500K) dataset of cancer mutations, all of which
> fall in coding regions. In the format I was given, the mutated positions
> are given as genomic (rather than CDS) coordinates. I noticed that the
> Ensembl REST API has a feature to map from protein to genomic coordinates (
> http://rest.ensembl.org/documentation/info/assembly_translation) but
> apparently not the other way round. What would be the simplest way to
> perform this kind of mapping?
>
> Many thanks,
> Greg
>
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