Problem with vcf2maf

Question

[zizigolu]

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?

Answer 1

[Ram]

As mentioned in the manual, you need to use the --vep-path to specify the path to VEP, not a VEP_PATH variable.

[zizigolu]

Thank you now saying catch is not finding

[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 --vep-path /local/software/ensembl-vep/95/vep
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

-------------------- EXCEPTION --------------------
MSG: ERROR: No cache found for homo_sapiens, version 95

STACK Bio::EnsEMBL::VEP::CacheDir::dir /home/local/software/ensembl-vep/95/vep/modules/Bio/EnsEMBL/VEP/CacheDir.pm:328
STACK Bio::EnsEMBL::VEP::CacheDir::init /home/local/software/ensembl-vep/95/vep/modules/Bio/EnsEMBL/VEP/CacheDir.pm:227
STACK Bio::EnsEMBL::VEP::CacheDir::new /home/local/software/ensembl-vep/95/vep/modules/Bio/EnsEMBL/VEP/CacheDir.pm:111
STACK Bio::EnsEMBL::VEP::AnnotationSourceAdaptor::get_all_from_cache /home/local/software/ensembl-vep/95/vep/modules/Bio/EnsEMBL/VEP/AnnotationSourceAdaptor.pm:115
STACK Bio::EnsEMBL::VEP::AnnotationSourceAdaptor::get_all /home/local/software/ensembl-vep/95/vep/modules/Bio/EnsEMBL/VEP/AnnotationSourceAdaptor.pm:93
STACK Bio::EnsEMBL::VEP::BaseRunner::get_all_AnnotationSources /home/local/software/ensembl-vep/95/vep/modules/Bio/EnsEMBL/VEP/BaseRunner.pm:175
STACK Bio::EnsEMBL::VEP::Runner::init /home/local/software/ensembl-vep/95/vep/modules/Bio/EnsEMBL/VEP/Runner.pm:123
STACK Bio::EnsEMBL::VEP::Runner::run /home/local/software/ensembl-vep/95/vep/modules/Bio/EnsEMBL/VEP/Runner.pm:194
STACK toplevel /local/software/ensembl-vep/95/vep/vep:225
Date (localtime)    = Mon Apr 15 16:13:00 2019
Ensembl API version = 95
---------------------------------------------------

ERROR: Failed to run the VEP annotator! Command: /usr/bin/perl /local/software/ensembl-vep/95/vep/vep --species homo_sapiens --assembly GRCh37 --no_progress --no_stats --buffer_size 5000 --sift b --ccds --uniprot --hgvs --symbol --numbers --domains --gene_phenotype --canonical --protein --biotype --uniprot --tsl --variant_class --shift_hgvs 1 --check_existing --total_length --allele_number --no_escape --xref_refseq --failed 1 --vcf --flag_pick_allele --pick_order canonical,tsl,biotype,rank,ccds,length --dir /home/fi1d18/.vep --fasta /temp/hgig/fi1d18/hs37d5.fa --format vcf --input_file tests/test_strelka.vcf --output_file tests/test_strelka.vep.vcf --offline --pubmed --fork 4 --polyphen b --af --af_1kg --af_esp --af_gnomad --regulatory
[fi1d18@cyan01 mskcc-vcf2maf-b8f7eeb]$

[Ram]

Please make an effort to solve problems yourself by reading the error message(s) carefully

Could not load .tbi/.csi index of /home/fi1d18/ExAC_nonTCGA.r0.3.1.sites.vep.vcf.gz

and

MSG: ERROR: No cache found for homo_sapiens, version 95

[zizigolu]

It also saying cach not available but catch is here

[fi1d18@cyan01 example_results]$ cd /home/local/software/ensembl-vep/95/cache/
[fi1d18@cyan01 cache]$ ls
Plugins  homo_sapiens  homo_sapiens_merged  homo_sapiens_refseq  tmp

[Ram]

catch

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.

[zizigolu]

Yes that says put cach in export VEP_DATA=

I put

export VEP_DATA=$/home/local/software/ensembl-vep/95/cache/

But same error

-------------------- EXCEPTION --------------------
MSG: ERROR: No cache found for homo_sapiens, version 95

[Ram]

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.

[zizigolu]

Yes you right now running

Sorry

[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 --vep-path /local/software/ensembl-vep/95/vep --vep-data /home/local/software/ensembl-vep/95/cache/

Thank you for helping