Extracting variant counts from Gnomad genome VCFs
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16 months ago
storm1907 ▴ 30

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:

enter image description here

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!

gnomad • 488 views
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what is "a file like this" ? how is it different from a "normal VCF" ?

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without headers and GT, GQ etc. values

enter image description here

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6 months ago
Kalin ▴ 10

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.

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A Tool post is recommended over resurrecting many old threads.

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