Extracting variant counts from Gnomad genome VCFs

Question

[storm1907]

Hello, I need to extract counts of synonymous and functional variants from gnomad v.3.1 genomes https://gnomad.broadinstitute.org/downloads I already have downloaded these genomes, extracted only exomic regions, and extracted desired population (european women only)

at the moment my file looks like this:

I know, how to gen snp counts from normal VCFs (using SNPEff tool); but I wonder how to extract variant counts from a file like this

Thank you!

[Pierre Lindenbaum]

what is "a file like this" ? how is it different from a "normal VCF" ?

[storm1907]

without headers and GT, GQ etc. values

Answer 1

[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.

[ATpoint]

A Tool post is recommended over resurrecting many old threads.

[Kalin]

Thank you, I did it now