Question: gnomAD: query utilitites
0
gravatar for bsmith030465
4 months ago by
bsmith030465150
United States
bsmith030465150 wrote:

Hi,

I wanted to query the gnomAD database without having to download and configure the entire data. Is there a way gnomAD provides an API for programmatic access? For example, for a given variant id, I want to retrieve the Total 'Allele Count':

INPUT: '1-978628-C-T' (or 'rs116586548')
OUTPUT: 180

i.e. if we query the website (gnomAD

I have thousands of variants that I want to get the Total Allele Count for, but would prefer not to download the entire dataset.

thanks!

gnomad • 314 views
ADD COMMENTlink modified 4 months ago by Garan580 • written 4 months ago by bsmith030465150
3
gravatar for Pierre Lindenbaum
4 months ago by
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum122k wrote:

use an API like https://myvariant.info/

wget -q -O - "http://myvariant.info/v1/variant/rs116586548" H  "accept: application/json"  
(..)
    "an": {
      "an": 30864,
      "an_afr": 8690,
      "an_amr": 838,
      "an_asj": 302,
      "an_eas": 1622,
      "an_female": 13804,
      "an_fin": 3490,
      "an_male": 17060,
      "an_nfe": 14940,
      "an_oth": 982,
      "an_popmax": 8690,
      "an_raw": 30990
    },

(...)
ADD COMMENTlink written 4 months ago by Pierre Lindenbaum122k
1
gravatar for manuel.belmadani
4 months ago by
Canada
manuel.belmadani1.1k wrote:

I don't think so, at least not officially. You might be able to find a third party web application that has gnomAD data.

Bravo is another variant database that seems to use part of the ExAC browser codebase: https://bravo.sph.umich.edu/freeze5/hg38/ and they provide an API. The data might not be as rich as gnomAD but it might be enough depending on what you need.

Varsome is a commerical variant database that might work here too: https://varsome.com/information/varsome-api-info/ which is free with some restrictions but also provides some premium models. They provide a sample client API as well: https://github.com/saphetor/varsome-api-client-python

There's some other solutions: https://bioinformatics.stackexchange.com/questions/933/is-there-public-restful-api-for-gnomad I couldn't get the tabix one to work though (the URL is different now, but still didn't work in my case.)

ADD COMMENTlink written 4 months ago by manuel.belmadani1.1k
1

tabix doesn't work anymore because the server for gnomad doesn't support "range-query" anymore.

ADD REPLYlink written 4 months ago by Pierre Lindenbaum122k
0
gravatar for Garan
4 months ago by
Garan580
United Kingdom
Garan580 wrote:

The Cellbase Swagger restful API might have what you're after, although I'm not sure how many requests it will take if you're looking to bulk query.

http://bioinfo.hpc.cam.ac.uk/cellbase/webservices/

http://bioinfo.hpc.cam.ac.uk/cellbase/webservices/rest/v4/hsapiens/feature/variation/rs116586548/info?limit=-1&skip=-1&skipCount=false&count=false&Output%20format=json

populationFrequencies   
0   
study   "GNOMAD_EXOMES"
population  "ALL"
refAllele   "C"
altAllele   "T"
refAlleleFreq   0.99945223
altAlleleFreq   0.00054777955
refHomGenotypeFreq  0.99890447
hetGenotypeFreq 0.0010955591
altHomGenotypeFreq  0
1   
study   "GNOMAD_EXOMES"
population  "OTH"
refAllele   "C"
altAllele   "T"
refAlleleFreq   0.9998051
altAlleleFreq   0.00019493178
refHomGenotypeFreq  0.9996101
hetGenotypeFreq 0.00038986356
altHomGenotypeFreq  0
ADD COMMENTlink written 4 months ago by Garan580
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1097 users visited in the last hour