Entering edit mode
5.0 years ago
zizigolu
★
4.3k
Hi,
I am trying to run vcf2maf software; In our cluster VEP has been installed in /local/software/ensembl-vep/95/vep. VEP is required by vcf2maf but wgen I am running vcf2maf can not find vep
[fi1d18@cyan01 mskcc-vcf2maf-b8f7eeb]$ export VEP_PATH=$/local/software/ensembl-vep/95/vep
[fi1d18@cyan01 mskcc-vcf2maf-b8f7eeb]$ perl vcf2maf.pl --input-vcf tests/test_strelka.vcf --output-maf tests/test.vep.maf --filter-vcf /home/fi1d18/ExAC_nonTCGA.r0.3.1.sites.vep.vcf.gz --ref-fasta /temp/hgig/fi1d18/hs37d5.fa
Could not load .tbi/.csi index of /home/fi1d18/ExAC_nonTCGA.r0.3.1.sites.vep.vcf.gz
WARNING: Reference allele C at MT:12418 doesn't match A (flanking bps: CAA) from reference FASTA: /temp/hgig/fi1d18/hs37d5.fa
STATUS: Running VEP and writing to: tests/test_strelka.vep.vcf
ERROR: Cannot find VEP script in path: /home/fi1d18/vep
Could somebody please help me telling vcf2maf where vep is?
Thank you now saying catch is not finding
Please make an effort to solve problems yourself by reading the error message(s) carefully
and
It also saying cach not available but catch is here
Surely, you mean
cache
. Did you read the manual page I pointed to? It contains the solution in the exact same line I picked the original solution from. Please do not continue threads without investing a decent level of effort first.Yes that says put cach in export VEP_DATA=
I put
But same error
No, it does not say that. You seem to be following instructions for people that do not have VEP installed (not what I pointed to) while you clearly have VEP installed (which is what I pointed to).
When pointed to the solution, please follow it all the way through. Requiring hand-holding to this extent is extremely unhealthy.
Yes you right now running
Sorry
Thank you for helping