Exome Aggregation Consortium (ExAC) database ?

Question

[Pierre Lindenbaum]

Dear lazyweb,

I wonder how data are stored behind the Exac server http://exac.broadinstitute.org/ :

• SQL only ?
• SQL+tabix/VCF ?
• Gemini ?
• ...

Thanks.

Pierre

[Ram]

"Dear lazyweb": Yet another indicator that Pierre *owns* BioStars :)

Answer 1

[Brad Chapman]

Pierre;

The source code is here:

https://github.com/konradjk/exac_browser

It looks like a MongoDB database and Python Flask webserver. It also builds on xBrowse:

https://github.com/xbrowse/xbrowse

[Pierre Lindenbaum]

ah yes thank you Brad, there's even a python script to load the tabix+vcf files: https://github.com/konradjk/exac_browser/blob/master/exac.py

(...)
def load_variants_file():
def load_variants(sites_file, i, n, db):
variants_generator = parse_tabix_file_subset([sites_file], i, n, get_variants_from_sites_vcf)
try:
db.variants.insert(variants_generator, w=0)
except pymongo.errors.InvalidOperation:
pass # handle error when variant_generator is empty