VEP: MSG: ERROR: Cannot use format vcf without Bio::DB::HTS::Tabix module installed

Question

[Filago]

Hello everybody, I want to annotate a VCF file with vep (v. 104). I installed VEP and everything works fine. However, when using the --custom flag and a gnomAD.vcf file to annotate allele frequencies, I get the following error message:

VEP: MSG: ERROR: Cannot use format vcf without Bio::DB::HTS::Tabix module installed

I reinstalled VEP and the problem still occurs.

Furthermore, after screening the internet, I tried

export PERL5LIB=/home/username/ensembl-vep/Bio/DB/HTS

as the Tabix.pm remains there --- but withouta any success.

Thank you for any advice or help!

Andreas

Answer 1

[Ben Moore]

Hi Andreas,

Could you please check that the Bio::DB::HTS::Tabix module is located in the ensembl-vep directory at /ensembl-vep/Bio/DB/HTS/Tabix.pm. Could you also check that your ensembl-vep folder is included in your PERL5LIB. If not, you can add it using export PERL5LIB=${PERL5LIB}:$ENSEMBL-VEP_PATH (where $ENSEMBL-VEP_PATH is the path to your ensembl-vep directory).

If none of this works, you may need to install htslib and Bio::DB::HTS manually.

[Filago]

Hey Ben!

I am still struggling with this issue. ensembl-vep is already in my @INC and the Tabix.pm is also at the right location.

Any ideas how to go further?

Best,

Andreas