Deleted:gnomADc plugin instructions not working for VEP
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4 weeks ago
Mk ▴ 10

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;

GRCh38 and gnomAD genomes:\

genomes="https://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/#chrom\tpos/; 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 "https://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.

gnomad gnomadc vep plugin ensembl • 70 views
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