VEP allele frequency from gnomAD genomes

Question

[milwaukee]

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?

[josloc]

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

[milwaukee]

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

[dario.garvan]

Yes, but that's gnomAD 2, which is an inferior lift-over to hg38, not gnomAD 3, which is read alignment to hg38. gnomAD 3 doesn't offer a single VCF file which would be useful for VEP.

[bjwiley23]

this is available since 2 years ago https://ftp.ensembl.org/pub/data_files/homo_sapiens/GRCh38/variation_genotype/gnomad/r3.0

Version 3 is the genomes

Answer 1

[Emily]

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.

[milwaukee]

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?

[Emily]

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.