GnomAD API Query Tool

Tl; dr, I love to tell a good story. If you don’t wanna read that, no worries. Just skip ahead or get straight to business!

Now, to the story.

I have been working on a project where I was using population allelic frequencies for about 6,000 SNPs (single nucleotide polymorphisms) for CEU (North Americans from UTAH with European ancestry) individuals from the 1000 Genomes Project. We have our own copy of this dataset in our computer, and it’s relatively straightforward to get those frequencies from vcf files. All good.

Then, I decided I should check whether CEU individuals were a good proxy for allelic frequencies in Europeans (excluding Finnish, which due to their interesting demographic history are usually excluded for this kind of analysis). I wanted to do this by comparing the allelic frequencies for CEU from the 1000 Genomes (404 individuals) to the tens of thousands ‘non-Finnish European’ samples from the the Genome Aggregation Database (gnomAD). Hence, I went to their website and thought to myself that downloading their entire dataset and calculating allelic frequencies did not strike me as elegant. Neigther did the idea of manually quering ~6,000 SNP IDs on the gnomAD browser (which is great if you only have a few SNPs to look at). No batch submission option was available.

There must be a well-established gnomAD API query tool available, right? Wrong! No such tool. Of course, I did find some solutions people made here and there, but none of them did exactly what I wanted.

Enters Michelle Enos, who is an awesome web developper and is entirely foreign to the field of computational biology. I explained what I needed and they made the tool I needed in javascript (which I am not fluent in). Modest, @crankysparrow thought this wasn’t much, ‘a fun little project’. But looking at biostars ¹, I begged to differ: we NEED this!

Even cooler, after they did the hard work, I was able to tweek the script to include some options that computational biologists would appreciate. Feedback is appreciated.

So here it is, from us, to you. A gnomAD API query tool that gathers gnomad-genomes or gnomad-exomes allelic frequencies for a list of SNP IDs for a population defined by the user. Link here. Enjoy!

A brief tutorial:

Requirements:

*node must be installed

*command line

*npm must be installed

Note: instructions available at the repo.

Input file

This should be a .json file with the SNP IDs you would like to query. IF you have a regular text file with one ID per line, you can use our conversion tool:

node scripts/readIDs.js --input path/<your_text_file_with_SNP_ids>.txt

This will produce an output file with the same name, but ending in ‘.json’. Then you can run:

node scripts/gnomad_query.js --input input/<our_SNP_IDs>.json --pop 'NFE' --db 'GNOMAD'

Enjoy!