Using VEP custom on ClinVar error - Couldn't find index.
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Entering edit mode
5 months ago
milwaukee • 0

Hi, Biostars community.

I have installed VEP docker container (ensemblorg/ensembl-vep), trying to use it for annotate my .vcf file with "--custom" option, but it doesn't work.

Usage command:

sudo docker run \
    -t -i -v ~/.vep:/opt/vep/.vep \
    ensemblorg/ensembl-vep vep \
    -i test.vcf --o result.vcf --custom clinvar.vcf.gz,ClinVar,vcf,exact,0,CLNSIG

~/.vep folder:

enter image description here

Error message:

[E::hts_open_format] Failed to open file clinvar.vcf.gz
Couldn't find index for file clinvar.vcf.gz at /usr/local/lib/x86_64-linux-gnu/perl/5.26.1/Bio/DB/HTS/Tabix.pm line 53.

UPD:

Thanks to VEP developer Andrew, problem is solved.

Solution was in changing paths inside of docker vep call.

sudo docker run \
    -t -i -v ~/.vep:/opt/vep/.vep \
    ensemblorg/ensembl-vep vep \
    -i /opt/vep/.vep/test.vcf --o /opt/vep/.vep/result.vcf --custom /opt/vep/.vep/clinvar.vcf.gz,ClinVar,vcf,exact,0,CLNSIG
vep custom ensembl clinvar • 391 views
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Entering edit mode

Is /home/gene the home directory for the account you are logged in? Can you explicitly add -v /home/gene/.vep instead of ~/.vep?

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Yes, it is. Still the same error.

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Entering edit mode
5 months ago

Cross-posted to GitHub with response from VEP developers: post

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