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Question: Can't find position in GnomAD VCF
1
gravatar for bzg
20 months ago by
bzg • 40
Brazil
bzg • 40 wrote:

I have a set of 700 mutations that I need to download from GnomAD. My first problem was: the mutation rs489693 can be found in the browser but it is not present in the VCF file (gnomad.genomes.r2.1.1.sites.18.vcf.bgz).

I searched also by the position 57882787.

Why this mutation is not present in the VCF file, but can be found via browsing? I believe I am missing some important concept. I hope someone can help me.
gnomad snv vcf • 667 views
ADD COMMENT • link •
modified 20 months ago by zx8754 ♦ 9.9k • written 20 months ago by bzg • 40
3
gravatar for Pierre Lindenbaum
20 months ago by
Pierre Lindenbaum ♦ 132k
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum ♦ 132k wrote:

I've got it. in gnomad.genomes.r2.1.sites.vcf.gz (release-181127)

$ bcftools view  gnomad.genomes.r2.1.sites.vcf.gz "18:57882787" | grep -v "##" | cut -f 1,2,3

#CHROM  POS ID
18  57882787    rs489693
ADD COMMENT • link modified 20 months ago • written 20 months ago by Pierre Lindenbaum ♦ 132k

You used the complete vcf. I used only the 18th chromosome. Maybe that is the reason.

ADD REPLY • link modified 20 months ago • written 20 months ago by bzg • 40

No, I found it using chr18:

$ wget -q -O - "https://storage.googleapis.com/gnomad-public/release/2.1.1/vcf/genomes/gnomad.genomes.r2.1.1.sites.18.vcf.bgz" | gunzip -c | cut -f 1,2,3 | grep 57882787 -m1
18  57882787    rs489693
ADD REPLY • link written 20 months ago by Pierre Lindenbaum ♦ 132k

thanks Pierre for taking your time to test it! The only difference I could conceive is the way I uncompressed the file. I used the nautilus utility. I realized that the size is much smaller (73Gb) while uncompressing with gunzip (100Gb).

ADD REPLY • link written 20 months ago by bzg • 40
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