[ensembl-dev] hgvs in offline mode.

Kurt Hetrick khetric1 at jhmi.edu
Mon Jan 4 17:54:43 GMT 2021


>From reading the online documentation I was under the impression that one could use hgvs in offline mode provided that they pointed to the fasta file, but the error I received suggests otherwise. Am I missing something or is hgvs not possible in offline mode. Using GRCh37.

I am using a singularity image for ensemble 102 that I pulled from a docker image that I built using the dockerfile from your dockerhub page where I changed the base image from Ubuntu 18.04 to Ubuntu 16.04 and then built the cache locally.

export PERL5LIB=/mnt/resources/vep_data
export PATH=$PATH:/mnt/resources/vep_data

singularity exec -B /mnt:/mnt /mnt/containers/vep-102.0.simg vep -i file2.txt -o test.vcf --fork 4 --cache --offline --refseq --force_overwrite --dir /mnt/resources/vep_data --fasta /mnt/research/tools/test/human_g1k_v37_decoy.fasta --hgvs --assembly GRCh37 --check_existing --dir_cache /mnt/resources/vep_data
2021-01-04 17:43:09 - INFO: BAM-edited cache detected, enabling --use_transcript_ref; use --use_given_ref to override this

-------------------- EXCEPTION --------------------
MSG: ERROR: Cannot use HGVS format in offline mode
STACK Bio::EnsEMBL::VEP::Parser::HGVS::new /opt/vep/src/ensembl-vep/modules/Bio/EnsEMBL/VEP/Parser/HGVS.pm:104
STACK Bio::EnsEMBL::VEP::Parser::new /opt/vep/src/ensembl-vep/modules/Bio/EnsEMBL/VEP/Parser.pm:151
STACK Bio::EnsEMBL::VEP::Runner::get_Parser /opt/vep/src/ensembl-vep/modules/Bio/EnsEMBL/VEP/Runner.pm:805
STACK Bio::EnsEMBL::VEP::Runner::get_InputBuffer /opt/vep/src/ensembl-vep/modules/Bio/EnsEMBL/VEP/Runner.pm:832
STACK Bio::EnsEMBL::VEP::Runner::init /opt/vep/src/ensembl-vep/modules/Bio/EnsEMBL/VEP/Runner.pm:140
STACK Bio::EnsEMBL::VEP::Runner::run /opt/vep/src/ensembl-vep/modules/Bio/EnsEMBL/VEP/Runner.pm:203
STACK toplevel /opt/vep/src/ensembl-vep/vep:229
Date (localtime)    = Mon Jan  4 17:43:09 2021
Ensembl API version = 102

head -n 5 file2.txt

Thanks in advance,

Kurt Hetrick

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