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.
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
[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.
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