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<p class="MsoNormal">Hello,<br>
<br>
>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.<br>
<br>
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.<br>
<br>
export PERL5LIB=/mnt/resources/vep_data<o:p></o:p></p>
<p class="MsoNormal">export PATH=$PATH:/mnt/resources/vep_data<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">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<o:p></o:p></p>
<p class="MsoNormal">2021-01-04 17:43:09 - INFO: BAM-edited cache detected, enabling --use_transcript_ref; use --use_given_ref to override this<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">-------------------- EXCEPTION --------------------<o:p></o:p></p>
<p class="MsoNormal">MSG: ERROR: Cannot use HGVS format in offline mode<o:p></o:p></p>
<p class="MsoNormal">STACK Bio::EnsEMBL::VEP::Parser::HGVS::new /opt/vep/src/ensembl-vep/modules/Bio/EnsEMBL/VEP/Parser/HGVS.pm:104<o:p></o:p></p>
<p class="MsoNormal">STACK Bio::EnsEMBL::VEP::Parser::new /opt/vep/src/ensembl-vep/modules/Bio/EnsEMBL/VEP/Parser.pm:151<o:p></o:p></p>
<p class="MsoNormal">STACK Bio::EnsEMBL::VEP::Runner::get_Parser /opt/vep/src/ensembl-vep/modules/Bio/EnsEMBL/VEP/Runner.pm:805<o:p></o:p></p>
<p class="MsoNormal">STACK Bio::EnsEMBL::VEP::Runner::get_InputBuffer /opt/vep/src/ensembl-vep/modules/Bio/EnsEMBL/VEP/Runner.pm:832<o:p></o:p></p>
<p class="MsoNormal">STACK Bio::EnsEMBL::VEP::Runner::init /opt/vep/src/ensembl-vep/modules/Bio/EnsEMBL/VEP/Runner.pm:140<o:p></o:p></p>
<p class="MsoNormal">STACK Bio::EnsEMBL::VEP::Runner::run /opt/vep/src/ensembl-vep/modules/Bio/EnsEMBL/VEP/Runner.pm:203<o:p></o:p></p>
<p class="MsoNormal">STACK toplevel /opt/vep/src/ensembl-vep/vep:229<o:p></o:p></p>
<p class="MsoNormal">Date (localtime) = Mon Jan 4 17:43:09 2021<o:p></o:p></p>
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<p class="MsoNormal" style="border:none;padding:0in">Ensembl API version = 102<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">head -n 5 file2.txt<o:p></o:p></p>
<p class="MsoNormal">NM_000492.4:c.-13_10del23<o:p></o:p></p>
<p class="MsoNormal">NM_000492.4:c.-9_14del23<o:p></o:p></p>
<p class="MsoNormal">NM_000492.4:c.-8G>C<o:p></o:p></p>
<p class="MsoNormal">NM_000492.4:c.[1046C>T;3747delG]<o:p></o:p></p>
<p class="MsoNormal">NM_000492.4:c.[1093_1094delCT;3705T>G]<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Thanks in advance,<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Kurt Hetrick<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
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