How to get minor allele frequencies from Exac?
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3.2 years ago
kynnjo ▴ 40

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.)

exac variants allele maf api • 1.4k views
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3.2 years ago

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

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@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.

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Hello,

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

fin swimmer

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

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