gnomAD v3 link not working for download
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:
However, I can use the same wget command to download GnomAD v2 and it works:
Can someone tell me what I am doing wrong with GnomADv3. Insights will be appreciated.
1 answer
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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link
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Pierre Lindenbaum
no, but you can always merge the vcfs using bcftools concat
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link
written
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Pierre Lindenbaum
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Don't know where you got that specific link from but
v. 3.1.1VCF files are available from gnomAD download page (look for appropriate tab),