Cannot find VEP script under
jingydz opened this issue · 1 comments
jingydz commented
$ perl vcf2maf.pl --input-vcf xxx.snp.vcf --output-maf test.maf --ref-fasta ../pig.dna.toplevel.fa
STATUS: Running VEP and writing to: xxx.snp.vep.vcf
ERROR: Cannot find VEP script under: /yyy/miniconda3/bin
allaway commented
Hello @jingydz, you can fix this using the --vep-path parameter.
For example, if you installed vep into a conda environment you could run:
find /. -name '*vep*' to locate vep.
You then might see something like
/opt/conda/envs/vcf2maf/bin/vep, which would mean you should run vcf2math with: --vep-path /opt/conda/envs/vcf2maf/bin/