Question: How to get minor allele frequencies from Exac?
0
gravatar for kynnjo
22 months ago by
kynnjo20
United States
kynnjo20 wrote:

I have ~70k dbSNP ids I need to get Exac minor allele counts and minor allele frequencies for.

Supposedly Exac provides this information for variants, but I can't find it, either in the JSON results obtainable through http://exac.hms.harvard.edu/rest or through Exac's web interface.

(BTW, the information needs to be from Exac, to be procedurally consistent with other annotations I'm working with.)

variants exac allele api maf • 939 views
ADD COMMENTlink modified 22 months ago by finswimmer13k • written 22 months ago by kynnjo20
2
gravatar for finswimmer
22 months ago by
finswimmer13k
Germany
finswimmer13k wrote:

Hello,

you can use the dbsnp endpoint from Exac's REST-API, or the variation endpoint from ensembl's REST-API. In both cases you have to parse the json for the allele frequencys to find out which allele is the minor one and what it's value.

fin swimmer

ADD COMMENTlink written 22 months ago by finswimmer13k

@finswimmer, thank you for your answer.

I was aware of the dbsnp endpoint from Exac's REST-API, but ruled it out as an option since it can handle only one dbSNP per query at a time. For my immediate task, I have ~70k such ids, and in the future I expect to deal with even larger numbers of them. I estimated (perhaps incorrectly) that a solution involving ~70k HTTP requests would be both slow on my end, and perhaps be not appreciated by the administrators server-side.

The second API you mentioned I had not considered at all, but it too can handle only one dbSNP per query.

I will investigate further to see if I can get this approach to work in a reasonable time.

ADD REPLYlink written 21 months ago by kynnjo20
1

Hello,

there is also an endpoint which can handle multiple variant ids.

fin swimmer

ADD REPLYlink written 21 months ago by finswimmer13k

@finswimmer: Thank you! That's extremely useful information. I'll try it out right now.

ADD REPLYlink written 21 months ago by kynnjo20
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