Can't find position in GnomAD VCF

Question

[Esther Brasil]

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.

Answer 1

[Pierre Lindenbaum]

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

[Esther Brasil]

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

[Pierre Lindenbaum]

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

[Esther Brasil]

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).