[ensembl-dev] Automate the SNP variant result from "population genetics"

[deepak kumar]

Hi Anja,

Thank you so much for the reply. It certainly helped me to get to the right
direction of my query. However, could you please help me understand a few
queries regarding the same:

To start of with, I find the "Rest API" a very clean approach to get
variant information.

a) My aim is to find if a SNP (rsID let say rs769971095) share populations,
or in other words, if this rsID mutation can be found in more than one
population. From the links you provided I see that I can find an answer but
am confused between "population allele frequency" and "population genotype
frequency". To fulfill my aim, data for this rsID should be taken from
"population allele frequency" or "population genotype frequency"?

b) The population name given in the "example output" of the "Rest API" are
in short form like 'AMR', 'SAS' etc. Could you please let me know how can i
retrieve the full population name for a given rsID?

Thanks much!
DK

On Tue, Sep 19, 2017 at 7:22 PM, Anja Thormann <anja at ebi.ac.uk> wrote:

> Hi DK,
>
> you have a few options of getting allele frequencies for a variant.
>
> You can use
>     - our perl API: http://www.ensembl.org/info/docs/api/variation/
> variation_tutorial.html#alleles (to get you started)
>     - our REST API: https://rest.ensembl.org/documentation/info/variation_
> id (to get you started)
>     - the VEP: https://www.ensembl.org/info/docs/tools/vep/script/
> vep_options.html It will allow you to annotate your input variants with
> frequency data if available
>
> Please feel free to contact us again if you have any questions regarding
> the above approaches.
>
> Kind regards,
> Anja
>
>
> On 19 Sep 2017, at 16:06, deepak kumar <deepak.k.choubey at gmail.com> wrote:
>
> Dear ALL,
>
>  I have been looking for a way to find "which nsSNP (with rs ID number
> like rs769971095) belong to what population(s), and if possible what
> gender"? I came to know about the Ensembl "population genetics" for the
> variants.
>
> I found the respective population genetics info for 2 rsIDs; rs559632360 &
> rs769971095
>
> For "rs769971095" the super-population it shows is: ALL, AFR, AMR, ASJ,
> EAS, FIN, NFE, OTH, SAS.
>
> For "rs559632360" the super-population it shows is: ALL, AFR, AMR, EAS,
> SAS, EUR.
>
>
> For rs559632360 rsID, it also shows population genetics from "1000 Genomes
> Project Phase 3 & gnomAD exomes" along with "subpopulation" information,
> whereas, for rs769971095 it shows only "gnomAD exomes" population genetics.
>
> http://grch37.ensembl.org/Homo_sapiens/Variation/Population?db=core;r=3:
> 12625875-12626875;v=rs769971095;vdb=variation;vf=135759093
>
> http://grch37.ensembl.org/Homo_sapiens/Variation/Population?db=core;r=3:
> 12632759-12633759;v=rs559632360;vdb=variation;vf=
> 92299087#population_freq_SAS
>
> Does this mean that for "rs769971095" there is no "1000 genomes project
> phase 3" data available?
>
> I am interested to know if these two rsIDs belong to one population, so,
> can it be said that these rsIDs share same population? If yes, what
> population they share? It would be great if I could know how to make a
> reasonable interpretation for this.
>
> Also, I need to do this for many rsIDs, could you please let me know how
> this process can be automated? Where, I can generate results like this:
>
>
> *rsID                  Super-Population with allele frequencies
>  Sub-population*
>
> rs769971095     ALL, AFR, AMR, ASJ, EAS, FIN, NFE, OTH, SAS.
>  .......etc
>
> rs559632360      ALL, AFR, AMR, EAS, SAS, EUR
>    ......etc
>
>
>
> Thanks much! DK
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