🔶 Retrieve gnomAD v4 data using python and export to csv

This repository is a fork of the broadinstitute/gnomad-browser repository with a GraphQL API query to retrieve specific data from gnomAD and save it as a csv.

Please head to this folder

• This is for using gnomAD's GraphQL API to retrieve allele frequencies, homozygote counts, and population specific numbers for your large list of variants (gnomAD v4 dataset).

• The folder contains a python file with a specific GraphQL API query with the population parameter set to Middle East (MID).

🟧 Requirements:

• Python

• Read python code with any code editor such as Visual Studio Code

• The requests python package is required. Open the command terminal and install the library by entering the following:

pip install requests

• time and csv libraries are part of the standard Python library.

🟧 Usage:

• Download the python file and open it in your code editor; install the necessary dependency.

• Prepare your list of VCF variants e.g.:

"2-123450-C-T",
"11-61364336-G-A",
"18-31598655-G-A"

Variants in HGVS nomenclature can be converted to VCF using VariantValidator's batch tool, among many other tools and APIs.

• Paste your variants in the variants variable in the python file.

• Run the code.

  • You will see the results outputted in the terminal. It will look something like this:

Variant ID: 2-233760233-C-CAT
Chromosome: 2
Position: 233760233
Reference: C
Alternate: CAT

Exome Data:
  Allele Count (AC): 395737
  Allele Number (AN): 1315438
  Homozygote Count: 22055
  Allele Frequency (AF): 0.30084048050915363

Genome Data:
  Allele Count (AC): 52299
  Allele Number (AN): 151162
  Homozygote Count: 9162
  Allele Frequency (AF): 0.34597980974054326

Joint Data:
  Allele Count (AC): 448036
  Allele Number (AN): 1466600
  Homozygote Count: 31217
  Allele Frequency (AF): 0.30549297695349786

Middle Eastern Population Data:
  Allele Count (AC): 1259
  Allele Number (AN): 4002
  Homozygote Count: 78
  Allele Frequency (AF): 0.31459270364817593

• There is a time buffer of 5 seconds between each variant to make sure the code does not end due to too many requests. If there is an error, it will wait longer and retry a few times.

• Once your full list of variants have been checked, it will save the results into an csv file named gnomadresults.csv This file will look something like this:

Variant	Exome Homozygote count	Exome AF	Genome Homozygote count	Genome AF	Joint Homozygote count	Joint AF	Middle Eastern Homozygote count	Middle Eastern AF
19-35848318-C-T	0	0	0	6.57E-06	0	6.20E-07	0	0
5-161873196-G-A	0	0	0	0	0	0	0	0
17-31261733-C-T	0	1.37E-06	0	6.57E-06	0	1.86E-06	0	0

If you find this useful, please feel free to use and modify as you see fit.

🟧 Citation

As mentioned by the gnomad-browser repository, please cite the following if you use gnomAD data:

• The mutational constraint spectrum quantified from variation in 141,456 humans
• The ExAC browser: displaying reference data information from over 60 000 exomes