extract gnomAD (exome/genome) all variant list in a specific gene (hg19)
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7 months ago
cocchi.e89 ▴ 170

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!

gnomAD human hg19 • 219 views
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7 months ago
4galaxy77 ▴ 990

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

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