Including tbi file along with VCF when running VEP on remote dataset (GnomadV3)
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6 weeks ago
maria2019 ▴ 200

Hi,

I am trying to run VEP on remote data from GnomadV3. I was hoping to run it remotely, without the need to download the dataset. However, when I try to run it remotely, I get an error that VEP cannot find the tbi file. Is there a way to include it in the code?

    vep -i input.vcf -o out.vcf --vcf --cache --force_overwrite\
 --custom https://gnomad-public-us-east-1.s3.amazonaws.com/release/3.1.2/vcf/genomes/gnomad.genomes.v3.1.2.sites.chr6.vcf.bgz,gnomADg,vcf,exact,0,AF,AF_afr,AF_amr,AF_asj,AF_eas,AF_fin,AF_nfe,AF_oth

Thanks!

VCF VEP gnomad annotation • 552 views
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tbi is just indexing of your vcf and it doesn't require to include in the code. Just index your tbi in the same directory where your vcf file is.

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I understand that. The problem is the files are not local. I am trying to reach the VCF and index file from https://gnomad.broadinstitute.org/downloads without downloading them

I need a way to redirect the code to the location of the index file.

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Unfortunately, there's no way to point the VEP to a different dir, the tbi files have to be in the same directory.

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thanks for your response

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