extract gnomAD (exome/genome) all variant list in a specific gene (hg19)

Question

[cocchi.e89]

I am working on some annotation on human WGS/WES data and I was wondering if there is a fast web-based way to extract a list of all variants listed in gnomAD in a specific gene (I can retrieve coordinates through UCSC in case). I'd need to avoid download all DB for this!

Thank you in advance for any help!

Answer 1

[4galaxy77]

If you don't want to download the whole dataset, then you can stream it directly through bcftools and then subset your variants if they are in a list like:

bcftools view -T list.txt https://storage.googleapis.com/gcp-public-data--gnomad/release/2.1.1/vcf/genomes/gnomad.genomes.r2.1.1.sites.vcf.bgz

Or query the annotations you want in the same way using bcftools query

Answer 2

[Kalin]

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_DB I have precomputed SQLite databases for gnomAD WGS for GRCh37/38 in the description of the package. Please take a look there.