<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="">I noticed that you are not using the supported VEP code. You can install the new code by following the instructions here: <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></div><div class=""><br class=""></div><div class="">The new VEP code supports annotations against a GFF or GTF file: <a href="http://www.ensembl.org/info/docs/tools/vep/script/vep_options.html#other" class="">http://www.ensembl.org/info/docs/tools/vep/script/vep_options.html#other</a></div><div class=""><br class=""></div><div class="">Anja</div><div class=""><br class=""><div><br class=""><blockquote type="cite" class=""><div class="">On 16 Jan 2018, at 14:06, Shawn Yost <<a href="mailto:yostshawn@gmail.com" class="">yostshawn@gmail.com</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><div dir="ltr" class=""><span style="font-size:12.8px" class="">Hi,</span><div style="font-size:12.8px" class="">I would like to annotate my VCF file against a custom transcript database. I've created both a GFF v3 file and a GTF file (see below) and I have been unsuccessful in getting VEP to annotate against these transcripts. The examples below are before using sort + bgzip + tabix (so that is not the problem).</div><div style="font-size:12.8px" class=""><br class=""></div><div style="font-size:12.8px" class="">I'm currently running VEP v85.</div><div style="font-size:12.8px" class=""><br class=""></div><div style="font-size:12.8px" class="">The command I used was:</div><div style="font-size:12.8px" class=""><a href="http://variant_effect_predictor.pl/" target="_blank" class="">variant_effect_predictor.pl</a> -i IN.vcf --custom test.gff.gz,,gff -fasta test.fa --cache -o OUT -dir /path/to/cache --hgvs --cache_version 75 --offline --force_overwrite<br class=""></div><div style="font-size:12.8px" class=""><br class=""></div><div style="font-size:12.8px" class="">In the outputted file I only see ENSTs and can't find the transcripts I inputted along with them.  The same thing occurs if I run --custom test.gtf.gz,,gtf.  If I change the command to --custom test.gtf.gz,,gtf,overlap it will tell me if it overlaps the inputted transcript but it doesn't annotate against the transcript.</div><div style="font-size:12.8px" class=""><br class=""></div><div style="font-size:12.8px" class=""><br class=""></div><div style="font-size:12.8px" class="">Is there a problem with the command options I am using? Is there a problem with the inputted files?  How do I get VEP to annotate the variant against my custom transcript (i.e. 412662  2:73613056      A       GENE1  TRANSCRIPT1 Transcript      synonymous_variant ....)?</div><div style="font-size:12.8px" class=""><br class=""></div><div style="font-size:12.8px" class=""><br class=""></div><div style="font-size:12.8px" class=""><br class=""></div><div style="font-size:12.8px" class="">Example output:</div><div style="font-size:12.8px" class="">241004  2:73613032-73613049     -       ENSG00000116127 ENST00000264448 Transcript      inframe_deletion        147-164 36-53   12-18       LEEEEEE/L       ctGGAGGAGGAGGAGGAGGAg/ctg       -      IMPACT=MODERATE;STRAND=1;<wbr class="">HGVSc=ENST00000264448.6:c.36_<wbr class="">53delNNNNNNNNNNNNNNNNNN;HGVSp=<wbr class="">ENSP00000264448.6:p.Glu23_<wbr class="">Glu28del</div><div style="font-size:12.8px" class=""><div class="">412662  2:73613056      A       ENSG00000116127 ENST00000377715 Transcript      synonymous_variant      171     60      20      E  gaG/gaA  -      IMPACT=LOW;STRAND=1;HGVSc=<wbr class="">ENST00000377715.1:c.60N>A;<wbr class="">HGVSp=ENST00000377715.1:c.60N><wbr class="">A(p.%3D)</div><div class="">412662  2:73613056      A       ENSG00000116127 ENST00000409009 Transcript      synonymous_variant      171     60      20      E  gaG/gaA  -      IMPACT=LOW;STRAND=1;HGVSc=<wbr class="">ENST00000409009.1:c.60N>A;<wbr class="">HGVSp=ENST00000409009.1:c.60N><wbr class="">A(p.%3D)</div><div class="">412662  2:73613056      A       ENSG00000116127 ENST00000264448 Transcript      synonymous_variant      171     60      20      E  gaG/gaA  -  IMPACT=LOW;STRAND=1;HGVSc=<wbr class="">ENST00000264448.6:c.60N>A;<wbr class="">HGVSp=ENST00000264448.6:c.60N><wbr class="">A(p.%3D)</div></div><div style="font-size:12.8px" class="">402364  2:73613066-73613071     -       ENSG00000116127 ENST00000377715 Transcript      inframe_deletion        181-186 70-75   24-25       EE/-    GAGGAA/-        -       IMPACT=MODERATE;STRAND=1;<wbr class="">HGVSc=ENST00000377715.1:c.70_<wbr class="">75delNNNNNN;HGVSp=<wbr class="">ENSP00000366944.1:p.Glu27_<wbr class="">Glu28del</div><div style="font-size:12.8px" class=""><br class=""></div><div style="font-size:12.8px" class=""><br class=""></div><div style="font-size:12.8px" class=""><br class=""></div><div style="font-size:12.8px" class="">GFF v3 file:</div><div style="font-size:12.8px" class=""><div class="">15      .       transcript      74701625        74726300        .       -       .       ID=TRANSCRIPT1;Alias=10741;<wbr class="">Name=SEMA7A<br class=""></div><div class=""><div class="">15      .       exon    74726082        74726300        .       -       .       ID=EXON37A10411.1;Parent=<wbr class="">TRANSCRIPT1</div><div class="">15      .       exon    74711142        74711293        .       -       .       ID=EXON37A10411.2;Parent=<wbr class="">TRANSCRIPT1</div><div class="">15      .       exon    74710609        74710650        .       -       .       ID=EXON37A10411.3;Parent=<wbr class="">TRANSCRIPT1</div><div class="">15      .       exon    74710218        74710310        .       -       .       ID=EXON37A10411.4;Parent=<wbr class="">TRANSCRIPT1</div><div class="">15      .       exon    74709932        74710016        .       -       .       ID=EXON37A10411.5;Parent=<wbr class="">TRANSCRIPT1</div><div class="">15      .       exon    74709676        74709786        .       -       .       ID=EXON37A10411.6;Parent=<wbr class="">TRANSCRIPT1</div><div class="">15      .       exon    74708916        74709055        .       -       .       ID=EXON37A10411.7;Parent=<wbr class="">TRANSCRIPT1</div><div class="">15      .       exon    74708142        74708326        .       -       .       ID=EXON37A10411.8;Parent=<wbr class="">TRANSCRIPT1</div><div class="">15      .       exon    74707179        74707287        .       -       .       ID=EXON37A10411.9;Parent=<wbr class="">TRANSCRIPT1</div><div class="">15      .       exon    74706888        74707086        .       -       .       ID=EXON37A10411.10;Parent=<wbr class="">TRANSCRIPT1</div><div class="">15      .       exon    74704226        74704353        .       -       .       ID=EXON37A10411.11;Parent=<wbr class="">TRANSCRIPT1</div><div class="">15      .       exon    74703897        74704051        .       -       .       ID=EXON37A10411.12;Parent=<wbr class="">TRANSCRIPT1</div><div class="">15      .       exon    74703636        74703697        .       -       .       ID=EXON37A10411.13;Parent=<wbr class="">TRANSCRIPT1</div><div class="">15      .       exon    74701625        74703326        .       -       .       ID=EXON37A10411.14;Parent=<wbr class="">TRANSCRIPT1</div><div class="">15      .       CDS     74726082        74726259        .       -       0       ID=CDS37A10411.1;Parent=<wbr class="">TRANSCRIPT1</div><div class="">15      .       CDS     74711142        74711293        .       -       2       ID=CDS37A10411.2;Parent=<wbr class="">TRANSCRIPT1</div><div class="">15      .       CDS     74710609        74710650        .       -       0       ID=CDS37A10411.3;Parent=<wbr class="">TRANSCRIPT1</div><div class="">15      .       CDS     74710218        74710310        .       -       0       ID=CDS37A10411.4;Parent=<wbr class="">TRANSCRIPT1</div><div class="">15      .       CDS     74709932        74710016        .       -       0       ID=CDS37A10411.5;Parent=<wbr class="">TRANSCRIPT1</div><div class="">15      .       CDS     74709676        74709786        .       -       2       ID=CDS37A10411.6;Parent=<wbr class="">TRANSCRIPT1</div><div class="">15      .       CDS     74708916        74709055        .       -       2       ID=CDS37A10411.7;Parent=<wbr class="">TRANSCRIPT1</div><div class="">15      .       CDS     74708142        74708326        .       -       0       ID=CDS37A10411.8;Parent=<wbr class="">TRANSCRIPT1</div><div class="">15      .       CDS     74707179        74707287        .       -       1       ID=CDS37A10411.9;Parent=<wbr class="">TRANSCRIPT1</div><div class="">15      .       CDS     74706888        74707086        .       -       0       ID=CDS37A10411.10;Parent=<wbr class="">TRANSCRIPT1</div><div class="">15      .       CDS     74704226        74704353        .       -       2       ID=CDS37A10411.11;Parent=<wbr class="">TRANSCRIPT1</div><div class="">15      .       CDS     74703897        74704051        .       -       0       ID=CDS37A10411.12;Parent=<wbr class="">TRANSCRIPT1</div><div class="">15      .       CDS     74703636        74703697        .       -       1       ID=CDS37A10411.13;Parent=<wbr class="">TRANSCRIPT1</div><div class="">15      .       CDS     74702965        74703326        .       -       2       ID=CDS37A10411.14;Parent=<wbr class="">TRANSCRIPT1</div></div></div><div style="font-size:12.8px" class=""><br class=""></div><div style="font-size:12.8px" class=""><br class=""></div><div style="font-size:12.8px" class="">GTF file:</div><div style="font-size:12.8px" class=""><div class="">TRANSCRIPT1    15   -       74701624        74726300        74702964        74726259        14      74701624,74703635,74703896,<wbr class="">74704225,74706887,74707178,<wbr class="">74708141,74708915,74709675,<wbr class="">74709931,74710217,74710608,<wbr class="">74711141,74726081,      74703326,74703697,74704051,<wbr class="">74704353,74707086,74707287,<wbr class="">74708326,74709055,74709786,<wbr class="">74710016,74710310,74710650,<wbr class="">74711293,74726300,      0       HGNC:10741      cmplcmpl    1,2,0,1,0,2,0,1,1,0,0,0,1,0,</div><div class="">TRANSCRIPT2    17   -       8108048 8113944 8108188 8113542 9       8108048,8108533,8109808,<wbr class="">8110067,8110493,8110888,<wbr class="">8111055,8113494,8113847,    8108362,8108708,8109957,<wbr class="">8110206,8110685,8110943,<wbr class="">8111158,8113567,8113944,        0       HGNC:11390      cmpl    cmpl0,2,0,2,2,1,0,0,-1,</div><div class="">TRANSCRIPT3    11   -       73711325        73720282        73712456        73718087        7       73711325,73714871,73715528,<wbr class="">73716774,73717213,73717961,<wbr class="">73720022,     73712571,73715052,73715630,<wbr class="">73716978,73717424,73718182,<wbr class="">73720282, 0       HGNC:12519      cmplcmpl    2,1,1,1,0,0,-1,</div><div class="">TRANSCRIPT4    11   -       123594634       123612391       123596704       123601596       9       123594634,123598183,123598840,<wbr class="">123599833,123600322,123601194,<wbr class="">123610824,123611124,123612256,  123597699,123598303,<wbr class="">123598970,123599922,123600533,<wbr class="">123601693,123610900,123611244,<wbr class="">123612391,  0       HGNC:12994      cmpl    cmpl    1,1,0,1,0,0,-1,-1,-1,</div><div class="">TRANSCRIPT5    19   -       51994480        52005043        51994894        52004987        8       51994480,52000133,52000602,<wbr class="">52001271,52002423,52002691,<wbr class="">52003173,52004560,    51995083,52000230,52000699,<wbr class="">52001541,52002471,52002970,<wbr class="">52003554,52005043,        0  HGNC:15482       cmpl    cmpl    0,2,1,1,1,1,1,0,</div><div class="">TRANSCRIPT6    1    +       228194722       228248972       228194829       228247166       4       228194722,228210367,228238356,<wbr class="">228246686,    228194900,228210609,<wbr class="">228238622,228248972,        0       HGNC:15983      cmpl    cmpl    0,2,1,0,</div></div><div style="font-size:12.8px" class=""><br class=""></div><div style="font-size:12.8px" class=""><br class=""></div><div style="font-size:12.8px" class=""><br class=""></div><div style="font-size:12.8px" class=""><br class=""></div><div style="font-size:12.8px" class=""><br class=""></div><div style="font-size:12.8px" class=""><br class=""></div><div style="font-size:12.8px" class=""><br class=""></div><div style="font-size:12.8px" class=""><div class="">Thank you for your help,</div><div class="">  Shawn</div></div><div class="gmail-yj6qo" style="font-size:12.8px"></div><div class="gmail-adL" style="font-size:12.8px"><br class=""></div></div>
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