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mskcc / vcf2maf

Convert a VCF into a MAF, where each variant is annotated to only one of all possible gene isoforms
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maf2maf issue #358

Open parvathisudha opened 2 months ago

parvathisudha commented 2 months ago

Hi, I am trying to convert vcf files to maf files for an already annotated (VEP) vcf file. "vcf2maf.pl" worked fine with --inhibit-vep option. For the output maf file of vcf2maf.pl, do I need to run maf2maf.pl ?

When I try the maf2maf.pl code using already downloaded VEP and Cache directory, I am getting an error. VEP commands worked without any issues.

$ ``` perl maf2maf.pl --input-maf /path/vcf2maf_OUT/sample1_snvs_passed.vep.maf --output-maf /path/maf2maf_OUT/sample1_snvs_passed.maf --species homo_sapiens --ncbi-build GRCh38 --ref-fasta /path/Homo_sapiens_assembly38.fasta --vep-path /path/VEP/ensembl-vep-release-101 --vep-data /path/VEP/vep_101_cache STATUS: Running VEP and writing to: /tmp/IvAynywXhb/sample1_snvs_passed.vep.vep.vcf



-------------------- EXCEPTION --------------------
MSG: ERROR: SIFT not available

STACK Bio::EnsEMBL::VEP::AnnotationSource::Cache::Transcript::check_sift_polyphen /path/VEP/ensembl-vep-release-101/modules/Bio/EnsEMBL/VEP/AnnotationSource/Cache/Transcript.pm:168
STACK Bio::EnsEMBL::VEP::AnnotationSource::Cache::Transcript::new /path/VEP/ensembl-vep-release-101/modules/Bio/EnsEMBL/VEP/AnnotationSource/Cache/Transcript.pm:121
STACK Bio::EnsEMBL::VEP::CacheDir::get_all_AnnotationSources /path/VEP/ensembl-vep-release-101/modules/Bio/EnsEMBL/VEP/CacheDir.pm:150
STACK Bio::EnsEMBL::VEP::AnnotationSourceAdaptor::get_all_from_cache /path/VEP/ensembl-vep-release-101/modules/Bio/EnsEMBL/VEP/AnnotationSourceAdaptor.pm:121
STACK Bio::EnsEMBL::VEP::AnnotationSourceAdaptor::get_all /path/VEP/ensembl-vep-release-101/modules/Bio/EnsEMBL/VEP/AnnotationSourceAdaptor.pm:91
STACK Bio::EnsEMBL::VEP::BaseRunner::get_all_AnnotationSources /path/VEP/ensembl-vep-release-101/modules/Bio/EnsEMBL/VEP/BaseRunner.pm:170
STACK Bio::EnsEMBL::VEP::Runner::init /path/VEP/ensembl-vep-release-101/modules/Bio/EnsEMBL/VEP/Runner.pm:132
STACK Bio::EnsEMBL::VEP::Runner::run /path/VEP/ensembl-vep-release-101/modules/Bio/EnsEMBL/VEP/Runner.pm:203
STACK toplevel path/VEP/ensembl-vep-release-101/vep:228
Date (localtime)    = Thu Jul 11 10:42:41 2024
Ensembl API version = 101
---------------------------------------------------

ERROR: Failed to run the VEP annotator!

Thanks!
Parvathi.