Describe the issue
VEP give errors even my query and reference has same assembly version
Command :$: ./vep -i examples/homo_sapiens_GRCh37.vcf –cache –refseq
cache reference details while running install.pl
? 458
NB: Remember to use –refseq when running the VEP with this cache!
- downloading ftp.ensembl.org/pub/release-104/variation/indexed_vep_cache/homo_sapiens_refseq_vep_104_GRCh37.tar.gz
- unpacking homo_sapiens_refseq_vep_104_GRCh37.tar.gz
- converting cache, this may take some time but will allow VEP to look up variants and frequency data much faster
- use CTRL-C to cancel if you do not wish to convert this cache now (you may run convert_cache.pl later)
2021-09-15 18:17:16 – Processing homo_sapiens_refseq
2021-09-15 18:17:16 – Processing version 104_GRCh37
2021-09-15 18:17:16 – INFO: BAM-edited cache detected, enabling –use_transcript_ref; use –use_given_ref to override this
2021-09-15 18:17:16 – No unprocessed types remaining, skipping
2021-09-15 18:17:16 – All done!
Additional information
Please fill in the following sections to help us find the source of your issue as quickly as possible.
System
-Ensemble version: 104
- Perl version: 5.26
- OS: Ubuntu
- tabix installed yes Version: 1.13
Full VEP command line
./vep -i examples/homo_sapiens_GRCh37.vcf --cache --refseq
### Full error message
-------------------- EXCEPTION --------------------
MSG: ERROR: Cache assembly version (GRCh37) and database or selected assembly version (GRCh38) do not match
You can use --offline to avoid a database connection entirely
STACK Bio::EnsEMBL::VEP::CacheDir::dir /home/krunal/Krunal/Software/ensembl-vep/modules/Bio/EnsEMBL/VEP/CacheDir.pm:340
STACK Bio::EnsEMBL::VEP::CacheDir::init /home/krunal/Krunal/Software/ensembl-vep/modules/Bio/EnsEMBL/VEP/CacheDir.pm:227
STACK Bio::EnsEMBL::VEP::CacheDir::new /home/krunal/Krunal/Software/ensembl-vep/modules/Bio/EnsEMBL/VEP/CacheDir.pm:111
STACK Bio::EnsEMBL::VEP::AnnotationSourceAdaptor::get_all_from_cache /home/krunal/Krunal/Software/ensembl-vep/modules/Bio/EnsEMBL/VEP/AnnotationSourceAdaptor.pm:115
STACK Bio::EnsEMBL::VEP::AnnotationSourceAdaptor::get_all /home/krunal/Krunal/Software/ensembl-vep/modules/Bio/EnsEMBL/VEP/AnnotationSourceAdaptor.pm:91
STACK Bio::EnsEMBL::VEP::BaseRunner::get_all_AnnotationSources /home/krunal/Krunal/Software/ensembl-vep/modules/Bio/EnsEMBL/VEP/BaseRunner.pm:170
STACK Bio::EnsEMBL::VEP::Runner::init /home/krunal/Krunal/Software/ensembl-vep/modules/Bio/EnsEMBL/VEP/Runner.pm:128
STACK Bio::EnsEMBL::VEP::Runner::run /home/krunal/Krunal/Software/ensembl-vep/modules/Bio/EnsEMBL/VEP/Runner.pm:199
STACK toplevel ./vep:232
Date (localtime) = Wed Sep 15 21:34:51 2021
Ensembl API version = 104
---------------------------------------------------
### Data files (if applicable)
i used default example file
examples/homo_sapiens_GRCh37.vcf
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