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

Anja Thormann anja at ebi.ac.uk
Tue Sep 19 17:22:52 BST 2017


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 <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 <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 <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=3:12625875-12626875;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 <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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