<html><head><meta http-equiv="Content-Type" content="text/html; charset=us-ascii"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class="">Hi Shawn,<div class=""><br class=""></div><div class=""><div class="">the Bio::DB::HTS module should have been installed by INSTALL.pl. Did you set the DYLD_LIBRARY_PATH environment variable as asked during the installation?</div><div class=""><br class=""></div><div class="">You can also install Bio::DB::HTS manually: <a href="https://github.com/Ensembl/Bio-DB-HTS" class="">https://github.com/Ensembl/Bio-DB-HTS</a>.</div><div class=""><br class=""></div><div class="">Anja</div><div><br class=""><blockquote type="cite" class=""><div class="">On 18 Jan 2018, at 14:46, Shawn Yost <<a href="mailto:yostshawn@gmail.com" class="">yostshawn@gmail.com</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><div class="">Hi,<br class="">I've installed the latest version of vep and I'm not getting a new<br class="">error. This error occurred also during the install/test step of vep:<br class=""><br class="">-------------------- EXCEPTION --------------------<br class="">MSG: ERROR: Cannot use format gff without Bio::DB::HTS::Tabix module installed<br class=""><br class="">STACK Bio::EnsEMBL::VEP::AnnotationSource::File::new<br class="">/mnt/scratch/DGE/GENSUSC/syost/vep/ensembl-vep/modules/Bio/EnsEMBL/VEP/AnnotationSource/File.pm:162<br class="">STACK Bio::EnsEMBL::VEP::AnnotationSourceAdaptor::get_all_custom<br class="">/mnt/scratch/DGE/GENSUSC/syost/vep/ensembl-vep/modules/Bio/EnsEMBL/VEP/AnnotationSourceAdaptor.pm:228<br class="">STACK Bio::EnsEMBL::VEP::AnnotationSourceAdaptor::get_all<br class="">/mnt/scratch/DGE/GENSUSC/syost/vep/ensembl-vep/modules/Bio/EnsEMBL/VEP/AnnotationSourceAdaptor.pm:93<br class="">STACK Bio::EnsEMBL::VEP::BaseRunner::get_all_AnnotationSources<br class="">/mnt/scratch/DGE/GENSUSC/syost/vep/ensembl-vep/modules/Bio/EnsEMBL/VEP/BaseRunner.pm:175<br class="">STACK Bio::EnsEMBL::VEP::Runner::init<br class="">/mnt/scratch/DGE/GENSUSC/syost/vep/ensembl-vep/modules/Bio/EnsEMBL/VEP/Runner.pm:123<br class="">STACK Bio::EnsEMBL::VEP::Runner::next_output_line<br class="">/mnt/scratch/DGE/GENSUSC/syost/vep/ensembl-vep/modules/Bio/EnsEMBL/VEP/Runner.pm:356<br class="">STACK toplevel ./t/Runner.t:739<br class="">Date (localtime) = Thu Jan 18 14:26:33 2018<br class="">Ensembl API version = 91<br class=""><br class=""><br class=""><br class="">I'm using a conda env to install/run VEP. Inside of the<br class="">'ensembl-vep/' directory Tabix does exist:<br class=""><br class=""><blockquote type="cite" class="">ls -la Bio/DB/HTS/Tabix*<br class=""></blockquote>-rw-rw---- 1 syost cancgene 6721 Jan 18 14:24 Bio/DB/HTS/Tabix.pm<br class=""><br class="">Bio/DB/HTS/Tabix:<br class="">total 12<br class="">drwxrwx--- 2 syost cancgene 4096 Jan 18 14:24 .<br class="">drwxrwx--- 5 syost cancgene 4096 Jan 18 14:24 ..<br class="">-rw-rw---- 1 syost cancgene 2974 Jan 18 14:24 Iterator.pm<br class=""><br class=""><br class="">I've also installed Tabix separately and it works. Do you have any<br class="">suggestions? Why isn't it recognizing the Tabix.pm?<br class=""><br class=""><br class="">Thanks,<br class=""> Shawn<br class=""><br class=""><br class=""><br class=""><br class="">On Tue, Jan 16, 2018 at 2:21 PM, Anja Thormann <<a href="mailto:anja@ebi.ac.uk" class="">anja@ebi.ac.uk</a>> wrote:<br class=""><blockquote type="cite" class="">Hi Shawn,<br class=""><br class="">I noticed that you are not using the supported VEP code. You can install the<br class="">new code by following the instructions here:<br class=""><a href="http://www.ensembl.org/info/docs/tools/vep/script/vep_download.html" class="">http://www.ensembl.org/info/docs/tools/vep/script/vep_download.html</a><br class=""><br class="">The new VEP code supports annotations against a GFF or GTF file:<br class="">http://www.ensembl.org/info/docs/tools/vep/script/vep_options.html#other<br class=""><br class="">Anja<br class=""><br class=""><br class="">On 16 Jan 2018, at 14:06, Shawn Yost <yostshawn@gmail.com> wrote:<br class=""><br class="">Hi,<br class="">I would like to annotate my VCF file against a custom transcript database.<br class="">I've created both a GFF v3 file and a GTF file (see below) and I have been<br class="">unsuccessful in getting VEP to annotate against these transcripts. The<br class="">examples below are before using sort + bgzip + tabix (so that is not the<br class="">problem).<br class=""><br class="">I'm currently running VEP v85.<br class=""><br class="">The command I used was:<br class="">variant_effect_predictor.pl -i IN.vcf --custom test.gff.gz,,gff -fasta<br class="">test.fa --cache -o OUT -dir /path/to/cache --hgvs --cache_version 75<br class="">--offline --force_overwrite<br class=""><br class="">In the outputted file I only see ENSTs and can't find the transcripts I<br class="">inputted along with them. The same thing occurs if I run --custom<br class="">test.gtf.gz,,gtf. If I change the command to --custom<br class="">test.gtf.gz,,gtf,overlap it will tell me if it overlaps the inputted<br class="">transcript but it doesn't annotate against the transcript.<br class=""><br class=""><br class="">Is there a problem with the command options I am using? Is there a problem<br class="">with the inputted files? How do I get VEP to annotate the variant against<br class="">my custom transcript (i.e. 412662 2:73613056 A GENE1<br class="">TRANSCRIPT1 Transcript synonymous_variant ....)?<br class=""><br class=""><br class=""><br class="">Example output:<br class="">241004 2:73613032-73613049 - ENSG00000116127 ENST00000264448<br class="">Transcript inframe_deletion 147-164 36-53 12-18<br class="">LEEEEEE/L ctGGAGGAGGAGGAGGAGGAg/ctg -<br class="">IMPACT=MODERATE;STRAND=1;HGVSc=ENST00000264448.6:c.36_53delNNNNNNNNNNNNNNNNNN;HGVSp=ENSP00000264448.6:p.Glu23_Glu28del<br class="">412662 2:73613056 A ENSG00000116127 ENST00000377715 Transcript<br class="">synonymous_variant 171 60 20 E gaG/gaA -<br class="">IMPACT=LOW;STRAND=1;HGVSc=ENST00000377715.1:c.60N>A;HGVSp=ENST00000377715.1:c.60N>A(p.%3D)<br class="">412662 2:73613056 A ENSG00000116127 ENST00000409009 Transcript<br class="">synonymous_variant 171 60 20 E gaG/gaA -<br class="">IMPACT=LOW;STRAND=1;HGVSc=ENST00000409009.1:c.60N>A;HGVSp=ENST00000409009.1:c.60N>A(p.%3D)<br class="">412662 2:73613056 A ENSG00000116127 ENST00000264448 Transcript<br class="">synonymous_variant 171 60 20 E gaG/gaA -<br class="">IMPACT=LOW;STRAND=1;HGVSc=ENST00000264448.6:c.60N>A;HGVSp=ENST00000264448.6:c.60N>A(p.%3D)<br class="">402364 2:73613066-73613071 - ENSG00000116127 ENST00000377715<br class="">Transcript inframe_deletion 181-186 70-75 24-25 EE/-<br class="">GAGGAA/- -<br class="">IMPACT=MODERATE;STRAND=1;HGVSc=ENST00000377715.1:c.70_75delNNNNNN;HGVSp=ENSP00000366944.1:p.Glu27_Glu28del<br class=""><br class=""><br class=""><br class="">GFF v3 file:<br class="">15 . transcript 74701625 74726300 . -<br class="">. ID=TRANSCRIPT1;Alias=10741;Name=SEMA7A<br class="">15 . exon 74726082 74726300 . - .<br class="">ID=EXON37A10411.1;Parent=TRANSCRIPT1<br class="">15 . exon 74711142 74711293 . - .<br class="">ID=EXON37A10411.2;Parent=TRANSCRIPT1<br class="">15 . exon 74710609 74710650 . - .<br class="">ID=EXON37A10411.3;Parent=TRANSCRIPT1<br class="">15 . exon 74710218 74710310 . - .<br class="">ID=EXON37A10411.4;Parent=TRANSCRIPT1<br class="">15 . exon 74709932 74710016 . - .<br class="">ID=EXON37A10411.5;Parent=TRANSCRIPT1<br class="">15 . exon 74709676 74709786 . - .<br class="">ID=EXON37A10411.6;Parent=TRANSCRIPT1<br class="">15 . exon 74708916 74709055 . - .<br class="">ID=EXON37A10411.7;Parent=TRANSCRIPT1<br class="">15 . exon 74708142 74708326 . - .<br class="">ID=EXON37A10411.8;Parent=TRANSCRIPT1<br class="">15 . exon 74707179 74707287 . - .<br class="">ID=EXON37A10411.9;Parent=TRANSCRIPT1<br class="">15 . exon 74706888 74707086 . - .<br class="">ID=EXON37A10411.10;Parent=TRANSCRIPT1<br class="">15 . exon 74704226 74704353 . - .<br class="">ID=EXON37A10411.11;Parent=TRANSCRIPT1<br class="">15 . exon 74703897 74704051 . - .<br class="">ID=EXON37A10411.12;Parent=TRANSCRIPT1<br class="">15 . exon 74703636 74703697 . - .<br class="">ID=EXON37A10411.13;Parent=TRANSCRIPT1<br class="">15 . exon 74701625 74703326 . - .<br class="">ID=EXON37A10411.14;Parent=TRANSCRIPT1<br class="">15 . CDS 74726082 74726259 . - 0<br class="">ID=CDS37A10411.1;Parent=TRANSCRIPT1<br class="">15 . CDS 74711142 74711293 . - 2<br class="">ID=CDS37A10411.2;Parent=TRANSCRIPT1<br class="">15 . CDS 74710609 74710650 . - 0<br class="">ID=CDS37A10411.3;Parent=TRANSCRIPT1<br class="">15 . CDS 74710218 74710310 . - 0<br class="">ID=CDS37A10411.4;Parent=TRANSCRIPT1<br class="">15 . CDS 74709932 74710016 . - 0<br class="">ID=CDS37A10411.5;Parent=TRANSCRIPT1<br class="">15 . CDS 74709676 74709786 . - 2<br class="">ID=CDS37A10411.6;Parent=TRANSCRIPT1<br class="">15 . CDS 74708916 74709055 . - 2<br class="">ID=CDS37A10411.7;Parent=TRANSCRIPT1<br class="">15 . CDS 74708142 74708326 . - 0<br class="">ID=CDS37A10411.8;Parent=TRANSCRIPT1<br class="">15 . CDS 74707179 74707287 . - 1<br class="">ID=CDS37A10411.9;Parent=TRANSCRIPT1<br class="">15 . CDS 74706888 74707086 . - 0<br class="">ID=CDS37A10411.10;Parent=TRANSCRIPT1<br class="">15 . CDS 74704226 74704353 . - 2<br class="">ID=CDS37A10411.11;Parent=TRANSCRIPT1<br class="">15 . CDS 74703897 74704051 . - 0<br class="">ID=CDS37A10411.12;Parent=TRANSCRIPT1<br class="">15 . CDS 74703636 74703697 . - 1<br class="">ID=CDS37A10411.13;Parent=TRANSCRIPT1<br class="">15 . CDS 74702965 74703326 . - 2<br class="">ID=CDS37A10411.14;Parent=TRANSCRIPT1<br class=""><br class=""><br class="">GTF file:<br class="">TRANSCRIPT1 15 - 74701624 74726300 74702964<br class="">74726259 14<br class="">74701624,74703635,74703896,74704225,74706887,74707178,74708141,74708915,74709675,74709931,74710217,74710608,74711141,74726081,<br class="">74703326,74703697,74704051,74704353,74707086,74707287,74708326,74709055,74709786,74710016,74710310,74710650,74711293,74726300,<br class="">0 HGNC:10741 cmplcmpl 1,2,0,1,0,2,0,1,1,0,0,0,1,0,<br class="">TRANSCRIPT2 17 - 8108048 8113944 8108188 8113542 9<br class="">8108048,8108533,8109808,8110067,8110493,8110888,8111055,8113494,8113847,<br class="">8108362,8108708,8109957,8110206,8110685,8110943,8111158,8113567,8113944,<br class="">0 HGNC:11390 cmpl cmpl0,2,0,2,2,1,0,0,-1,<br class="">TRANSCRIPT3 11 - 73711325 73720282 73712456<br class="">73718087 7<br class="">73711325,73714871,73715528,73716774,73717213,73717961,73720022,<br class="">73712571,73715052,73715630,73716978,73717424,73718182,73720282, 0<br class="">HGNC:12519 cmplcmpl 2,1,1,1,0,0,-1,<br class="">TRANSCRIPT4 11 - 123594634 123612391 123596704<br class="">123601596 9<br class="">123594634,123598183,123598840,123599833,123600322,123601194,123610824,123611124,123612256,<br class="">123597699,123598303,123598970,123599922,123600533,123601693,123610900,123611244,123612391,<br class="">0 HGNC:12994 cmpl cmpl 1,1,0,1,0,0,-1,-1,-1,<br class="">TRANSCRIPT5 19 - 51994480 52005043 51994894<br class="">52004987 8<br class="">51994480,52000133,52000602,52001271,52002423,52002691,52003173,52004560,<br class="">51995083,52000230,52000699,52001541,52002471,52002970,52003554,52005043,<br class="">0 HGNC:15482 cmpl cmpl 0,2,1,1,1,1,1,0,<br class="">TRANSCRIPT6 1 + 228194722 228248972 228194829<br class="">228247166 4 228194722,228210367,228238356,228246686,<br class="">228194900,228210609,228238622,228248972, 0 HGNC:15983 cmpl<br class="">cmpl 0,2,1,0,<br class=""><br class=""><br class=""><br class=""><br class=""><br class=""><br class=""><br class="">Thank you for your help,<br class=""> Shawn<br class=""><br class="">_______________________________________________<br class="">Dev mailing list Dev@ensembl.org<br class="">Posting guidelines and subscribe/unsubscribe info:<br class="">http://lists.ensembl.org/mailman/listinfo/dev<br class="">Ensembl Blog: http://www.ensembl.info/<br class=""><br class=""><br class=""><br class="">_______________________________________________<br class="">Dev mailing list Dev@ensembl.org<br class="">Posting guidelines and subscribe/unsubscribe info:<br class="">http://lists.ensembl.org/mailman/listinfo/dev<br class="">Ensembl Blog: http://www.ensembl.info/<br class=""><br class=""></blockquote>_______________________________________________<br class="">Dev mailing list <a href="mailto:Dev@ensembl.org" class="">Dev@ensembl.org</a><br class="">Posting guidelines and subscribe/unsubscribe info: <a href="http://lists.ensembl.org/mailman/listinfo/dev" class="">http://lists.ensembl.org/mailman/listinfo/dev</a><br class="">Ensembl Blog: <a href="http://www.ensembl.info/" class="">http://www.ensembl.info/</a><br class=""></div></div></blockquote></div><br class=""></div></body></html>