VEP allele frequency from gnomAD genomes

VEP allele frequency from gnomAD genomes

1

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.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

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