I am trying to annotate a vcf file with ~12k variants using the online VEP. I have tried different options and invariably it returns a table ONLY with "uploaded variant", "location" and "consequence" columns as results. No more annotation fields are populated through the process, and the relevant columns are filled by "-".
I have tried running VEP in docker. It seems this is working however it is super slow (maybe because I am not using
vep --species homo_sapiens --assembly GRCh38 --input_file in.vcf --output_file out_vep.txt --tab --verbose --database --everything --force_overwrite --fork 60
Any inputs on why online VEP doesn't do the job?