VEP allele frequency from gnomAD genomes
1
0
Entering edit mode
9 months ago
milwaukee • 0

Hi, Biostars community.

According to VEP documentation, gnomAD genomes database could be used with --custom option. Example from VEP dosc:

./vep -i examples/homo_sapiens_GRCh38.vcf --cache \ --custom gnomad.genomes.r2.0.1.sites.GRCh38.noVEP.vcf.gz,gnomADg,vcf,exact,0,AF_AFR,AF_AMR,AF_ASJ,AF_EAS,AF_FIN,AF_NFE,AF_OTH

But there is no gnomAD genomes file for all chromosomes on ensembl's ftp source: ftp://ftp.ensembl.org/pub/data_files/homo_sapiens/GRCh38/variation_genotype/gnomad/r2.1/genomes/

Only data separated by chromosome is presented.

Can someone explain me, how to merge given .vcf.gz files correctly?

vep allele frequency gnomad genomes • 973 views
ADD COMMENT
0
Entering edit mode

Hi....Have you found a source to download all sites for gnomaAD allele frequency data?? I am combining all chromosomes but it will take at least a week for my job to finish on our HPC thanks

ADD REPLY
0
Entering edit mode

Hi! Yes, AF included in data privided on gnomAD downloads page. BTW, if you interested in all chromosomes AF data, look at "All chromosomes sites VCF". https://gnomad.broadinstitute.org/downloads

ADD REPLY
3
Entering edit mode
9 months ago

If it's just the exomes you're after, the --af_gnomad option covers this. You only need the custom option to use the full genomes, but I will speak to the team about how this works for the full genomes.

ADD COMMENT
0
Entering edit mode

Thanks for quick reply.

But I really interested in using gnomAD genomes database in my project, is it possible to merge given .vcf.gz files and pass merged file to --custom option?

ADD REPLY
0
Entering edit mode

Ah, you said exomes so I got confused.

I've checked with our variation team and they suggest downloading directly from gnomAD. It is somewhat massive (743.06 GB). gnomAD changed how they released the files to us. We will update that documentation.

ADD REPLY

Login before adding your answer.

Traffic: 2384 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6