[ensembl-dev] Annotating variants against custom transcripts
Anja Thormann
anja at ebi.ac.uk
Tue Jan 16 14:21:15 GMT 2018
Hi Shawn,
I noticed that you are not using the supported VEP code. You can install the new code by following the instructions here: http://www.ensembl.org/info/docs/tools/vep/script/vep_download.html <http://www.ensembl.org/info/docs/tools/vep/script/vep_download.html>
The new VEP code supports annotations against a GFF or GTF file: http://www.ensembl.org/info/docs/tools/vep/script/vep_options.html#other <http://www.ensembl.org/info/docs/tools/vep/script/vep_options.html#other>
Anja
> On 16 Jan 2018, at 14:06, Shawn Yost <yostshawn at gmail.com> wrote:
>
> Hi,
> 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).
>
> I'm currently running VEP v85.
>
> The command I used was:
> variant_effect_predictor.pl <http://variant_effect_predictor.pl/> -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
>
> 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.
>
>
> 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 ....)?
>
>
>
> Example output:
> 241004 2:73613032-73613049 - ENSG00000116127 ENST00000264448 Transcript inframe_deletion 147-164 36-53 12-18 LEEEEEE/L ctGGAGGAGGAGGAGGAGGAg/ctg - IMPACT=MODERATE;STRAND=1;HGVSc=ENST00000264448.6:c.36_53delNNNNNNNNNNNNNNNNNN;HGVSp=ENSP00000264448.6:p.Glu23_Glu28del
> 412662 2:73613056 A ENSG00000116127 ENST00000377715 Transcript synonymous_variant 171 60 20 E gaG/gaA - IMPACT=LOW;STRAND=1;HGVSc=ENST00000377715.1:c.60N>A;HGVSp=ENST00000377715.1:c.60N>A(p.%3D)
> 412662 2:73613056 A ENSG00000116127 ENST00000409009 Transcript synonymous_variant 171 60 20 E gaG/gaA - IMPACT=LOW;STRAND=1;HGVSc=ENST00000409009.1:c.60N>A;HGVSp=ENST00000409009.1:c.60N>A(p.%3D)
> 412662 2:73613056 A ENSG00000116127 ENST00000264448 Transcript synonymous_variant 171 60 20 E gaG/gaA - IMPACT=LOW;STRAND=1;HGVSc=ENST00000264448.6:c.60N>A;HGVSp=ENST00000264448.6:c.60N>A(p.%3D)
> 402364 2:73613066-73613071 - ENSG00000116127 ENST00000377715 Transcript inframe_deletion 181-186 70-75 24-25 EE/- GAGGAA/- - IMPACT=MODERATE;STRAND=1;HGVSc=ENST00000377715.1:c.70_75delNNNNNN;HGVSp=ENSP00000366944.1:p.Glu27_Glu28del
>
>
>
> GFF v3 file:
> 15 . transcript 74701625 74726300 . - . ID=TRANSCRIPT1;Alias=10741;Name=SEMA7A
> 15 . exon 74726082 74726300 . - . ID=EXON37A10411.1;Parent=TRANSCRIPT1
> 15 . exon 74711142 74711293 . - . ID=EXON37A10411.2;Parent=TRANSCRIPT1
> 15 . exon 74710609 74710650 . - . ID=EXON37A10411.3;Parent=TRANSCRIPT1
> 15 . exon 74710218 74710310 . - . ID=EXON37A10411.4;Parent=TRANSCRIPT1
> 15 . exon 74709932 74710016 . - . ID=EXON37A10411.5;Parent=TRANSCRIPT1
> 15 . exon 74709676 74709786 . - . ID=EXON37A10411.6;Parent=TRANSCRIPT1
> 15 . exon 74708916 74709055 . - . ID=EXON37A10411.7;Parent=TRANSCRIPT1
> 15 . exon 74708142 74708326 . - . ID=EXON37A10411.8;Parent=TRANSCRIPT1
> 15 . exon 74707179 74707287 . - . ID=EXON37A10411.9;Parent=TRANSCRIPT1
> 15 . exon 74706888 74707086 . - . ID=EXON37A10411.10;Parent=TRANSCRIPT1
> 15 . exon 74704226 74704353 . - . ID=EXON37A10411.11;Parent=TRANSCRIPT1
> 15 . exon 74703897 74704051 . - . ID=EXON37A10411.12;Parent=TRANSCRIPT1
> 15 . exon 74703636 74703697 . - . ID=EXON37A10411.13;Parent=TRANSCRIPT1
> 15 . exon 74701625 74703326 . - . ID=EXON37A10411.14;Parent=TRANSCRIPT1
> 15 . CDS 74726082 74726259 . - 0 ID=CDS37A10411.1;Parent=TRANSCRIPT1
> 15 . CDS 74711142 74711293 . - 2 ID=CDS37A10411.2;Parent=TRANSCRIPT1
> 15 . CDS 74710609 74710650 . - 0 ID=CDS37A10411.3;Parent=TRANSCRIPT1
> 15 . CDS 74710218 74710310 . - 0 ID=CDS37A10411.4;Parent=TRANSCRIPT1
> 15 . CDS 74709932 74710016 . - 0 ID=CDS37A10411.5;Parent=TRANSCRIPT1
> 15 . CDS 74709676 74709786 . - 2 ID=CDS37A10411.6;Parent=TRANSCRIPT1
> 15 . CDS 74708916 74709055 . - 2 ID=CDS37A10411.7;Parent=TRANSCRIPT1
> 15 . CDS 74708142 74708326 . - 0 ID=CDS37A10411.8;Parent=TRANSCRIPT1
> 15 . CDS 74707179 74707287 . - 1 ID=CDS37A10411.9;Parent=TRANSCRIPT1
> 15 . CDS 74706888 74707086 . - 0 ID=CDS37A10411.10;Parent=TRANSCRIPT1
> 15 . CDS 74704226 74704353 . - 2 ID=CDS37A10411.11;Parent=TRANSCRIPT1
> 15 . CDS 74703897 74704051 . - 0 ID=CDS37A10411.12;Parent=TRANSCRIPT1
> 15 . CDS 74703636 74703697 . - 1 ID=CDS37A10411.13;Parent=TRANSCRIPT1
> 15 . CDS 74702965 74703326 . - 2 ID=CDS37A10411.14;Parent=TRANSCRIPT1
>
>
> GTF file:
> TRANSCRIPT1 15 - 74701624 74726300 74702964 74726259 14 74701624,74703635,74703896,74704225,74706887,74707178,74708141,74708915,74709675,74709931,74710217,74710608,74711141,74726081, 74703326,74703697,74704051,74704353,74707086,74707287,74708326,74709055,74709786,74710016,74710310,74710650,74711293,74726300, 0 HGNC:10741 cmplcmpl 1,2,0,1,0,2,0,1,1,0,0,0,1,0,
> TRANSCRIPT2 17 - 8108048 8113944 8108188 8113542 9 8108048,8108533,8109808,8110067,8110493,8110888,8111055,8113494,8113847, 8108362,8108708,8109957,8110206,8110685,8110943,8111158,8113567,8113944, 0 HGNC:11390 cmpl cmpl0,2,0,2,2,1,0,0,-1,
> TRANSCRIPT3 11 - 73711325 73720282 73712456 73718087 7 73711325,73714871,73715528,73716774,73717213,73717961,73720022, 73712571,73715052,73715630,73716978,73717424,73718182,73720282, 0 HGNC:12519 cmplcmpl 2,1,1,1,0,0,-1,
> TRANSCRIPT4 11 - 123594634 123612391 123596704 123601596 9 123594634,123598183,123598840,123599833,123600322,123601194,123610824,123611124,123612256, 123597699,123598303,123598970,123599922,123600533,123601693,123610900,123611244,123612391, 0 HGNC:12994 cmpl cmpl 1,1,0,1,0,0,-1,-1,-1,
> TRANSCRIPT5 19 - 51994480 52005043 51994894 52004987 8 51994480,52000133,52000602,52001271,52002423,52002691,52003173,52004560, 51995083,52000230,52000699,52001541,52002471,52002970,52003554,52005043, 0 HGNC:15482 cmpl cmpl 0,2,1,1,1,1,1,0,
> TRANSCRIPT6 1 + 228194722 228248972 228194829 228247166 4 228194722,228210367,228238356,228246686, 228194900,228210609,228238622,228248972, 0 HGNC:15983 cmpl cmpl 0,2,1,0,
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> Thank you for your help,
> Shawn
>
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