gnomAD v3 link not working for download
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4 weeks ago
peter ▴ 10

I am trying to download whole genome GnomAD vcf file but every time I do it gives me ERROR 404: Not found. This is how I am trying to download the data:

wget https://storage.googleapis.com/gnomad-public/release/3.0/vcf/genomes/gnomad.genomes.r3.0.sites.vcf.bgz

However, I can use the same wget command to download GnomAD v2 and it works:

wget https://storage.googleapis.com/gcp-public-data--gnomad/release/2.1.1/liftover_grch38/vcf/genomes/gnomad.genomes.r2.1.1.sites.liftover_grch38.vcf.bgz

Can someone tell me what I am doing wrong with GnomADv3. Insights will be appreciated.

GnomAD snp vcf • 349 views
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Don't know where you got that specific link from but v. 3.1.1 VCF files are available from gnomAD download page (look for appropriate tab),

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4 weeks ago

your URL is wrong.

$  wget -q -O - "https://storage.googleapis.com/gcp-public-data--gnomad/release/3.1.1/vcf/genomes/gnomad.genomes.v3.1.1.sites.chr1.vcf.bgz" | gunzip -c | head
##fileformat=VCFv4.2
##hailversion=0.2.64-1ef70187dc78
##FILTER=<ID=AC0,Description="Allele count is zero after filtering out low-confidence genotypes (GQ < 20; DP < 10; and AB < 0.2 for het calls)">
##FILTER=<ID=AS_VQSR,Description="Failed VQSR filtering thresholds of -2.7739 for SNPs and -1.0606 for indels (probabilities of being a true positive variant)">
##FILTER=<ID=InbreedingCoeff,Description="GATK InbreedingCoeff < -0.3">
##FILTER=<ID=PASS,Description="Passed all variant filters">
##INFO=<ID=AC,Number=A,Type=Integer,Description="Alternate allele count">
##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles">
##INFO=<ID=AF,Number=A,Type=Float,Description="Alternate allele frequency">
##INFO=<ID=popmax,Number=A,Type=String,Description="Population with maximum AF
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Thank you for your reply. I found this link too but its per chromosome. I was looking for all chromosome vcf like in gnomad v2. Gnomad v3 doesn't have all chromosomes vcf?

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no, but you can always merge the vcfs using bcftools concat

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Thank you @Piere this helped.

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