[ensembl-dev] Missing MAF numbers on VEP REST service

[Paul Flicek]

Hi Beat,

Could you give me some insight about what you are looking for in the 
case of SNPs with more than two alleles.  For example, what do you 
expect the MAF to return in these cases?

More specifically, MAF is not a property of a variant site itself.   
Frequency is a property of the various alleles.  We are currently 
loading and returning the dbSNP MAF for each SNP, which is defined as 
the frequency of the second most common allele, but in reality, the SNP 
has several alleles and each of them has a frequency.  As more 
individuals are assayed, more SNPs will be found to have 3 or 4 alleles, 
so this is an issue that will grow.

Thanks,
Paul	



On 31 Jul 2016, at 8:39, Wolf Beat wrote:

> Hello,
>
> i recently migrated a lot of my code from the biomart interface to the 
> ensembl rest service. I'm mainly using grch37 as my source.
> I made the following observation:
> When i query a multi allelic variant, the REST VEP service returns not 
> MAF numbers.
> But when i query the biomart service or check the variant on the 
> website manually, the MAF numbers are present.
> Just to give one example:
> Variant rs6687605 has an MAF number of 0.43 when looked at on the 
> website and biomart:
> http://grch37.ensembl.org/Homo_sapiens/Variation/Explore?r=1:25889132-25890132;v=rs6687605;vdb=variation;vf=106422589
>
> But the REST service returns no MAF number:
> http://grch37.rest.ensembl.org/vep/hsapiens/id/rs6687605?content-type=application/json
>
> I observed the same behaviour for:
> rs2229546, rs6022, rs1058111
>
> I also observed that the VEP rest service specifies:
> http://grch37.rest.ensembl.org/documentation/info/vep_id_get
> That the ExAC information is by default off. But i do recieve it 
> without specifying the option.
> In my case i actually want it, but its still interesting to note.
>
> The first problem is kind of a big issue for me, any help in solving 
> it would be greatly appreciated.
>
> Kind regards
>
> Beat Wolf
>
> _______________________________________________
> Dev mailing list    Dev at ensembl.org
> Posting guidelines and subscribe/unsubscribe info: 
> http://lists.ensembl.org/mailman/listinfo/dev
> Ensembl Blog: http://www.ensembl.info/