[ensembl-dev] VEP 76 gtf2vep

[Ksenia Krasileva]

Dear developers team,

I am working towards using a custom annotation of wheat genes in variant
effect prediction with VEP.

While building cache with gtf2vep.pl, I see that my exon and transcript
features are cached, but CDS features are most likely not read correctly
(gene biotype gets re-set to 'pseudogene' by fix_transcript and there is no
translation). VEP is able to use this cache but the prediction is not
correct as there is no translation or CDS.

I tried to de-bug by running gtf2vep.pl with an example single exon gene
from Ensembl annotation for Triticum aestivum. I tried both v22 and v23
annotations and both give me the same result as before - biotype gets
re-set to 'pseudogene' in cache and there is no CDS/translation. Attached
are two test input gtfs that I am using from
Triticum_aestivum.IWGSP1.22.gff3 and Triticum_aestivum.IWGSP1.23.gff3
respectively.

The command line is below:

perl gtf2vep.pl -i test.v23.gff -f IWGSC_CSS_AB-TGAC_v1.fa -d 23 -s
wheat_custom

I appreciate your suggestions of what might be going on.

Thank you in advance,

Ksenia


Ksenia Krasileva, PhD
USDA NIFA Post Doctoral Scholar
Department of Plant Sciences
University of California, Davis
124 Robbins Hall
Davis, CA 95616

Email: krasileva at ucdavis.edu
Twitter: @kseniakrasileva <https://twitter.com/kseniakrasileva>
Web: http://dubcovskylab.ucdavis.edu/lab-member/ksenia-v-krasileva
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mail.ensembl.org/pipermail/dev_ensembl.org/attachments/20140923/31fab595/attachment.html>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: test.v22.gff
Type: application/octet-stream
Size: 617 bytes
Desc: not available
URL: <http://mail.ensembl.org/pipermail/dev_ensembl.org/attachments/20140923/31fab595/attachment.obj>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: test.v23.gff
Type: application/octet-stream
Size: 1310 bytes
Desc: not available
URL: <http://mail.ensembl.org/pipermail/dev_ensembl.org/attachments/20140923/31fab595/attachment-0001.obj>