how to find the Allele Number of specific variant from gnomAD
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6 months ago
Sara ▴ 220

I am working with a dataset from gnomAD for which i need to find the "Allele Number" for the variant we are working on. I tried to find such information from this link:

https://gnomad.broadinstitute.org/downloads#v2-coverage

but it is not in those files. do you know from which file we can find Allele Number? here is a screenshot of the page showing some information (however I am looking for a file to extract required information including Allele Number):

gnomAD

gnomAD • 376 views
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6 months ago

The VCF files. column info: AN

$ wget -q -O - "https://storage.googleapis.com/gcp-public-data--gnomad/release/2.1.1/vcf/exomes/gnomad.exomes.r2.1.1.sites.22.vcf.bgz" | gunzip -c | grep ID=AN,
##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in samples">
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@PierreLindenbaum : Thanks. using this command I only get info about ancestries. but what I am looking for is the "Allele Number" for each variant. like the screenshot I attached in the question. do you know how I can get this number?

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re-read my answer please.

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