[ensembl-dev] Mapping genomic coordinates to CDS

[Greg Slodkowicz]

That's fantastic, thanks a lot!

Greg

On Thu, Nov 5, 2015 at 5:12 PM Will McLaren <wm2 at ebi.ac.uk> wrote:

> 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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