Hi,
I have been trying to use vcf2maf 1.6.9 with current Ensembl VEP (version 85) to convert vcf files to maf. My data is preprocessed using Ensembl 73. Therefore, I have installed older VEP cache 73 ftp://ftp.ensembl.org/pub/release-73/variation/VEP/homo_sapiens_refseq_vep_73.tar.gz. I had to use this file because the installation script of VEP release 73 tries to fetch cache from an empty directory.
The problem is that perl /share/apps/vcf2maf/1.6.9/vcf2maf.pl --input-vcf $vcfdir/out.vcf --output-maf $vcfdir/$targetname.maf --vcf-tumor-id tumor --vcf-normal-id control --vep-path /share/apps/vcf2maf/1.6.9/vep_path --vep-data /share/apps/vcf2maf/1.6.9/vep_data --cache-version 73 --ref-fasta $WRKDIR/Data/Homo_sapiens.GRCh37.73.dna.chr.fa produces the following error-
Unknown option: cache-version
I tried to overcome the issue by setting --vep-data to /share/apps/vcf2maf/1.6.9/vep_data/homo_sapiens/73 which produces another error:
Cache directory /share/apps/vcf2maf/1.6.9/vep_data/homo_sapiens/73/homo_sapiens not found.
Please, tell me how to set the cache path properly.
