VEP allele frequency from gnomAD genomes
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?
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