Hi,
I have installed VEP for offline use and I am trying to download the data for the gnomADc plugin. The instructions from VEP are as follows;
genomes=”storage.googleapis.com/gnomad-public/release/3.0/coverage/genomes”
genome_coverage_tsv=”gnomad.genomes.r3.0.coverage.summary.tsv.bgz”
wget “${genomes}/${genome_coverage_tsv}”
zcat “${genome_coverage_tsv}” | sed -e ‘1s/^locus/#chromtpos/; s/:/t/’ | bgzip > gnomADc.gz
tabix -s 1 -b 2 -e 2 gnomADc.gz
When I try to download the gnomAD coverage file using wget as suggested, I get a 404 error. I checked their github page and someone has already raised this issue and they have suggested an updated documentation for gnomad v2.1. I am interested in gnomad version 3.1 and found that the link from gnomad download pages “storage.googleapis.com/gcp-public-data–gnomad/release/3.0.1/coverage/genomes/gnomad.genomes.r3.0.1.coverage.summary.tsv.bgz“. Since they have update the processing commands I cannot use them directly. Has anyone encountered this issue and hopefully have a solution for this.
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