mskcc/vcf2maf

--ref-fasta missing or empty

Rozita1 opened this issue · 0 comments

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: https://gist.github.com/ckandoth/61c65ba96b011f286220fa4832ad2bc0

However, when I test vcf2maf using the command
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 mycd $HOME to another directory which has more space as my 'home directory' doesn't have enough space for all the files required by VEP.

Any suggestions as to what I could be doing wrong / how to fix this?

Many thanks.