ERROR: Failed to run the VEP annotator!

[EsterAH]

Hello, I'm trying to convert vcf file into MAF with vcf2maf, I have the environment with the packages installed, but whenever I try to convert a vcf file I got this error:
perl: warning: Falling back to the standard locale ("C").
Possible precedence issue with control flow operator at /home/earroba/miniconda3/envs/vcf2maf/lib/site_perl/5.26.2/Bio/DB/IndexedBase.pm line 805.
Unknown option: af_gnomad
ERROR: Failed to parse command-line flags

ERROR: Failed to run the VEP annotator!

The code I'm typing is something like this:
vcf2maf.pl --input-vcf /pathtothevcf/file.vcf --output-maf test.maf --normal-id NORMAL --tumor-id TUMOR --ref-fasta /pathtothereference/hg19.fa --vep-data /pathtovep/104_GRCh37 --vep-path ~/miniconda3/envs/vep/bin/ --ncbi-build GRCh37

Any idea of what is wrong in there???

Many thanks in advance!!!

[guodudou]

Hello, I have encountered similar ERROR. Have you had the problem fixed?

Thanks,
Wendy

[armish]

For future users, the solution to this problem is downgrading the VEP to 106.1:

$ conda install -c bioconda ensembl-vep=106.1

The af_gnomad argument is deprecated with the newer versions of VEP.