Question: VCF2MAF does not recognize option --cache-version
0
gravatar for kjnousia
2.5 years ago by
kjnousia0
kjnousia0 wrote:

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.

vcf2maf vep cache software error • 1.1k views
ADD COMMENTlink written 2.5 years ago by kjnousia0
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1500 users visited in the last hour