Hi,
I would like to run vcf2maf on my vcf files and I followed the instructions here https://github.com/mskcc/vcf2maf#quick-start and installed VEP using the instructions here:
However, when I test vcf2maf using the command (& the same is for all the subsequent commands that are written in the quickstart section for vcf2maf):
perl vcf2maf.pl --input-vcf tests/test.vcf --output-maf tests/test.vep.maf
I get the following error message:
ERROR: Provided --ref-fasta is missing or empty: $HOME/.vep/homo_sapiens/102_GRCh37/Homo_sapiens.GRCh37.dna.toplevel.fa.gz
even though when I check the folder it is there - I'm not sure what exactly is wrong. I've had to change the path for my $HOME to another directory which has more space as my 'home directory' doesn't have enough space for all the files required by VEP. I've even copied that file specifically to the same path in the home directory and yet I still got the same error message.
Any suggestions as to what I could be doing wrong / how to fix this?
Many thanks.
