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<p class="MsoNormal"><span style="color:#1F497D">Thanks Andrew,<br>
<br>
The part that led me to believe that using hgvs in offline mode was possible was in the vep options page, but maybe I was misreading them…based on your answer, using it for when the input is hgvs is not possible, but it might be possible for when you want to
annotate a file with hgvs and your input is not hgvs (which I also will want to do)…which I haven’t attempted yet, but plan to do so in the near future.<br>
<br>
https://m.ensembl.org/info/docs/tools/vep/script/vep_options.html<br>
<br>
for the --fasta and --hgvs flags.<o:p></o:p></span></p>
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<o:p></o:p></span></p>
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<pre style="margin-bottom:12.0pt;line-height:12.0pt"><span style="font-size:9.5pt;color:#333333">--fasta [file|dir]<o:p></o:p></span></pre>
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<pre style="margin-bottom:12.0pt;line-height:12.0pt;overflow-wrap: break-word"><span style="font-size:9.5pt;color:#333333">--fa<o:p></o:p></span></pre>
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<p class="MsoNormal" style="line-height:15.0pt"><span style="font-size:9.5pt;font-family:"Helvetica",sans-serif;color:#333333">Specify a FASTA file or a directory containing FASTA files to use to look up reference sequence. The first time you run VEP with this
parameter an index will be built which can take a few minutes. <b><span style="background:yellow;mso-highlight:yellow">This is required if fetching HGVS annotations</span></b> (<a href="https://m.ensembl.org/info/docs/tools/vep/script/vep_options.html#opt_hgvs"><span style="color:#33478C">--hgvs</span></a>) …<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="color:#1F497D"><o:p> </o:p></span></p>
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<pre style="margin-bottom:12.0pt;line-height:12.0pt"><span style="font-size:9.5pt;color:#333333">--hgvs<o:p></o:p></span></pre>
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<p class="MsoNormal" style="line-height:15.0pt"><span style="font-size:9.5pt;font-family:"Helvetica",sans-serif;color:#333333"> <o:p></o:p></span></p>
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<p class="MsoNormal" style="line-height:15.0pt"><span style="font-size:9.5pt;font-family:"Helvetica",sans-serif;color:#333333">Add <a href="https://varnomen.hgvs.org/" target="_blank"><span style="color:#33478C">HGVS</span></a> nomenclature based on Ensembl
stable identifiers to the output. Both coding and protein sequence names are added where appropriate.
<b><span style="background:yellow;mso-highlight:yellow">To generate HGVS identifiers when using <a href="https://m.ensembl.org/info/docs/tools/vep/script/vep_options.html#opt_cache"><span style="color:#33478C">--cache</span></a> or <a href="https://m.ensembl.org/info/docs/tools/vep/script/vep_options.html#opt_offline"><span style="color:#33478C">--offline</span></a> you
must use a FASTA file and <a href="https://m.ensembl.org/info/docs/tools/vep/script/vep_options.html#opt_fasta"><span style="color:#33478C">--fasta</span></a></span>.
</b>HGVS notations given on Ensembl identifiers are <a href="https://m.ensembl.org/info/genome/stable_ids/index.html"><span style="color:#33478C">versioned</span></a>. <i>Not used by default</i><o:p></o:p></span></p>
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<p class="MsoNormal" style="line-height:15.0pt"><span style="font-size:9.5pt;font-family:"Helvetica",sans-serif;color:#333333">HGVSc, HGVSp, HGVS_OFFSET<o:p></o:p></span></p>
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<p class="MsoNormal" style="line-height:15.0pt"><span style="font-size:9.5pt;font-family:"Helvetica",sans-serif;color:#333333"> <o:p></o:p></span></p>
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<pre style="margin-bottom:12.0pt;line-height:12.0pt;overflow-wrap: break-word"><span style="font-size:9.5pt;color:#333333">--hgvsg<o:p></o:p></span></pre>
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<p class="MsoNormal" style="line-height:15.0pt"><span style="font-size:9.5pt;font-family:"Helvetica",sans-serif;color:#333333"> <o:p></o:p></span></p>
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<p class="MsoNormal" style="line-height:15.0pt"><span style="font-size:9.5pt;font-family:"Helvetica",sans-serif;color:#333333">Add genomic <a href="https://varnomen.hgvs.org/" target="_blank"><span style="color:#33478C">HGVS</span></a> nomenclature based on
the input chromosome name. <b><span style="background:yellow;mso-highlight:yellow">To generate HGVS identifiers when using <a href="https://m.ensembl.org/info/docs/tools/vep/script/vep_options.html#opt_cache"><span style="color:#33478C">--cache</span></a> or <a href="https://m.ensembl.org/info/docs/tools/vep/script/vep_options.html#opt_offline"><span style="color:#33478C">--offline</span></a> you
must use a FASTA file and <a href="https://m.ensembl.org/info/docs/tools/vep/script/vep_options.html#opt_fasta"><span style="color:#33478C">--fasta</span></a></span>.</b> <i>Not used by default</i><o:p></o:p></span></p>
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<p class="MsoNormal"><span style="color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D"><br>
<br>
<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D">There are other parts of the online documentation that stated that it was not possible for various reasons, but the above is what led me to believe that it might be possible.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D">Best Regards,<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D">Kurt Hetrick<o:p></o:p></span></p>
<p class="MsoPlainText"><o:p> </o:p></p>
<p class="MsoPlainText">Message: 2<o:p></o:p></p>
<p class="MsoPlainText">Date: Mon, 4 Jan 2021 18:22:50 +0000<o:p></o:p></p>
<p class="MsoPlainText">From: Andrew Parton <<a href="mailto:aparton@ebi.ac.uk"><span style="color:windowtext;text-decoration:none">aparton@ebi.ac.uk</span></a>><o:p></o:p></p>
<p class="MsoPlainText">To: Ensembl developers list <<a href="mailto:dev@ensembl.org"><span style="color:windowtext;text-decoration:none">dev@ensembl.org</span></a>><o:p></o:p></p>
<p class="MsoPlainText">Subject: Re: [ensembl-dev] hgvs in offline mode.<o:p></o:p></p>
<p class="MsoPlainText">Message-ID: <<a href="mailto:DF835DE9-2062-4EB4-81AA-84798B69AA10@ebi.ac.uk"><span style="color:windowtext;text-decoration:none">DF835DE9-2062-4EB4-81AA-84798B69AA10@ebi.ac.uk</span></a>><o:p></o:p></p>
<p class="MsoPlainText">Content-Type: text/plain; charset="utf-8"<o:p></o:p></p>
<p class="MsoPlainText"><o:p> </o:p></p>
<p class="MsoPlainText">Hi Kurt,<o:p></o:p></p>
<p class="MsoPlainText"><o:p> </o:p></p>
<p class="MsoPlainText">Unfortunately the error is correct, you cannot use HGVS input format in offline mode.<o:p></o:p></p>
<p class="MsoPlainText"><o:p> </o:p></p>
<p class="MsoPlainText">If there?s something incorrect or unclear in our docs then I would like to update it, could you please point in the direction of the documentation you found?<o:p></o:p></p>
<p class="MsoPlainText"><o:p> </o:p></p>
<p class="MsoPlainText">Kind Regards,<o:p></o:p></p>
<p class="MsoPlainText">Andrew<o:p></o:p></p>
<p class="MsoPlainText"><o:p> </o:p></p>
<p class="MsoPlainText"><o:p> </o:p></p>
<p class="MsoPlainText"><o:p> </o:p></p>
<p class="MsoPlainText">> On 4 Jan 2021, at 17:54, Kurt Hetrick <<a href="mailto:khetric1@jhmi.edu"><span style="color:windowtext;text-decoration:none">khetric1@jhmi.edu</span></a>> wrote:<o:p></o:p></p>
<p class="MsoPlainText">><o:p> </o:p></p>
<p class="MsoPlainText">> Hello,<o:p></o:p></p>
<p class="MsoPlainText">><o:p> </o:p></p>
<p class="MsoPlainText">> 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.<o:p></o:p></p>
<p class="MsoPlainText">><o:p> </o:p></p>
<p class="MsoPlainText">> 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.<o:p></o:p></p>
<p class="MsoPlainText">><o:p> </o:p></p>
<p class="MsoPlainText">> export PERL5LIB=/mnt/resources/vep_data export <o:p></o:p></p>
<p class="MsoPlainText">> PATH=$PATH:/mnt/resources/vep_data<o:p></o:p></p>
<p class="MsoPlainText">><o:p> </o:p></p>
<p class="MsoPlainText">> singularity exec -B /mnt:/mnt /mnt/containers/vep-102.0.simg vep -i
<o:p></o:p></p>
<p class="MsoPlainText">> file2.txt -o test.vcf --fork 4 --cache --offline --refseq
<o:p></o:p></p>
<p class="MsoPlainText">> --force_overwrite --dir /mnt/resources/vep_data --fasta
<o:p></o:p></p>
<p class="MsoPlainText">> /mnt/research/tools/test/human_g1k_v37_decoy.fasta --hgvs --assembly
<o:p></o:p></p>
<p class="MsoPlainText">> GRCh37 --check_existing --dir_cache /mnt/resources/vep_data<o:p></o:p></p>
<p class="MsoPlainText">> 2021-01-04 17:43:09 - INFO: BAM-edited cache detected, enabling
<o:p></o:p></p>
<p class="MsoPlainText">> --use_transcript_ref; use --use_given_ref to override this<o:p></o:p></p>
<p class="MsoPlainText">><o:p> </o:p></p>
<p class="MsoPlainText">> -------------------- EXCEPTION --------------------<o:p></o:p></p>
<p class="MsoPlainText">> MSG: ERROR: Cannot use HGVS format in offline mode STACK
<o:p></o:p></p>
<p class="MsoPlainText">> Bio::EnsEMBL::VEP::Parser::HGVS::new <o:p></o:p></p>
<p class="MsoPlainText">> /opt/vep/src/ensembl-vep/modules/Bio/EnsEMBL/VEP/Parser/HGVS.pm:104<o:p></o:p></p>
<p class="MsoPlainText">> STACK Bio::EnsEMBL::VEP::Parser::new <o:p></o:p></p>
<p class="MsoPlainText">> /opt/vep/src/ensembl-vep/modules/Bio/EnsEMBL/VEP/Parser.pm:151<o:p></o:p></p>
<p class="MsoPlainText">> STACK Bio::EnsEMBL::VEP::Runner::get_Parser <o:p></o:p></p>
<p class="MsoPlainText">> /opt/vep/src/ensembl-vep/modules/Bio/EnsEMBL/VEP/Runner.pm:805<o:p></o:p></p>
<p class="MsoPlainText">> STACK Bio::EnsEMBL::VEP::Runner::get_InputBuffer <o:p></o:p></p>
<p class="MsoPlainText">> /opt/vep/src/ensembl-vep/modules/Bio/EnsEMBL/VEP/Runner.pm:832<o:p></o:p></p>
<p class="MsoPlainText">> STACK Bio::EnsEMBL::VEP::Runner::init <o:p></o:p></p>
<p class="MsoPlainText">> /opt/vep/src/ensembl-vep/modules/Bio/EnsEMBL/VEP/Runner.pm:140<o:p></o:p></p>
<p class="MsoPlainText">> STACK Bio::EnsEMBL::VEP::Runner::run <o:p></o:p></p>
<p class="MsoPlainText">> /opt/vep/src/ensembl-vep/modules/Bio/EnsEMBL/VEP/Runner.pm:203<o:p></o:p></p>
<p class="MsoPlainText">> STACK toplevel /opt/vep/src/ensembl-vep/vep:229<o:p></o:p></p>
<p class="MsoPlainText">> Date (localtime) = Mon Jan 4 17:43:09 2021<o:p></o:p></p>
<p class="MsoPlainText">> Ensembl API version = 102<o:p></o:p></p>
<p class="MsoPlainText">><o:p> </o:p></p>
<p class="MsoPlainText">> head -n 5 file2.txt<o:p></o:p></p>
<p class="MsoPlainText">> NM_000492.4:c.-13_10del23<o:p></o:p></p>
<p class="MsoPlainText">> NM_000492.4:c.-9_14del23<o:p></o:p></p>
<p class="MsoPlainText">> NM_000492.4:c.-8G>C<o:p></o:p></p>
<p class="MsoPlainText">> NM_000492.4:c.[1046C>T;3747delG]<o:p></o:p></p>
<p class="MsoPlainText">> NM_000492.4:c.[1093_1094delCT;3705T>G]<o:p></o:p></p>
<p class="MsoPlainText">><o:p> </o:p></p>
<p class="MsoPlainText">> Thanks in advance,<o:p></o:p></p>
<p class="MsoPlainText">><o:p> </o:p></p>
<p class="MsoPlainText">> Kurt Hetrick<o:p></o:p></p>
<p class="MsoPlainText">><o:p> </o:p></p>
<p class="MsoPlainText"><o:p> </o:p></p>
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