Is there an API for querying the Exac database?

Question

[brady.forcier1]

Hi,

I am trying to collect data on mutations from Exac without using the web browser aka. using an API to query the EXAC database and return data (like ensembl) Specifically, I want to be able to put in a chr location/variant and gather information on population frequencies, transcript, annotation etc. Not concerned with read data. (e.g.,) http://exac.broadinstitute.org/variant/7-143087637-C-T.

https://github.com/konradjk/exac_browser

This seems like it's just the source code for the Exac browser you use online as it has to run a local database server. It doesn't look like there's an API for making queries directly to the site, but is it possible to just download the database locally and run queries on it that way? I also am able to download the raw data via:

ftp://ftp.broadinstitute.org/pub/ExAC_release/release0.3/

Not sure how to analyze this data however.

Open to any suggestions. Thanks

[Pierre Lindenbaum]

please define "run queries ". if that's just getting variants in a region then tabix is enough. Other tools like GATK selectVariants or bcftools can do the job too.

[brady.forcier1]

To be more clear, I want to be able to put in a chr location/variant and gather information on population frequencies, transcript, annotation etc. Not concerned with read data. (eg) http://exac.broadinstitute.org/variant/7-143087637-C-T

Answer 1

[leekaiinthesky]

ExAC HMS added a REST API on top of the ExAC database. Very handy.

You can see examples here: http://exac.hms.harvard.edu/. e.g. http://exac.hms.harvard.edu/rest/dbsnp/<rsid>

One long-term caveat is ensuring that the database they're using is up to date relative to http://exac.broadinstitute.org/, but I don't think it's an issue at the moment.

[Rm]

looks like http://exac.hms.harvard.edu/ is down for quite some time