Quickly get allele frequencies from Gnomad
2
1
Entering edit mode
16 months ago
Floydian_slip ▴ 160

Hi, I would like to know the AF of ~4000 rsIDs (dbSNP) quickly in Gnomad GRCh37 database. I looked at the instructions for getting this from Gnomad and it seems I would need to download the entire data. Is there is a faster and less involved way fo getting the AF from Gnomad without downloading more than 50GB of data? Any script or API or another way to crawl Gnomad database? Thanks!

gnomad allele freq ngs • 1.8k views
ADD COMMENT
5
Entering edit mode
16 months ago
Ram 35k

The af-only-gnomad.raw.vcf file here is 13 GB. It might work better than the 80+ GB file from the gnomAD website.

ADD COMMENT
0
Entering edit mode

Thanks! this is perfect!

ADD REPLY
0
Entering edit mode

If an answer was helpful, you should upvote it; if the answer resolved your question, you should mark it as accepted. You can accept more than one answer if they all work.

Upvote|Bookmark|Accept

ADD REPLY
0
Entering edit mode
4 months ago
Kalin • 0

I created a python package based on SQLite databases, where you can easily query all gnomAD variants for GRCh37/38. https://github.com/KalinNonchev/gnomAD_MAF
I have precomputed SQLite databases for gnomAD WGS for GRCh37/38 in the description of the package. Please take a look there.

Best,

ADD COMMENT
0
Entering edit mode

Kalin : Please create a single tools post to announce your package. Don't post the same content in multiple old threads.

ADD REPLY

Login before adding your answer.

Traffic: 1785 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6