WARNING: Chromosome ? not found in annotation sources or synonyms on line ? about ensembl-vep HOT 2 CLOSED

Hi @jooY-Jeong,
Hope this meets you well?
To use docker with VEP, the instructions are here
To mount the cache resources volume, suggesting you run it this way
docker run -v $HOME/vep_data:/data ensemblorg/ensembl-vep \ vep --cache --offline --format vcf --vcf --force_overwrite \ --input_file input/my_input.vcf \ --output_file output/my_output.vcf \ --custom file=custom/my_extra_data.bed,short_name=BED_DATA,format=bed,type=exact,coords=1 \ --plugin NMD
Also suggesting you run VEP docker first and then the output can be used with VCF2MAF.
Please let us know if this helps
Thank you,
Ola.

from ensembl-vep.

Thank you for helping me again.

I'll try it as you said, and if there's another error, I'll be back. Thank you!

from ensembl-vep.