[ensembl-dev] How to add custom motifs and transcription factor binding sites to VEP

Will McLaren wm2 at ebi.ac.uk
Mon Oct 13 11:26:39 BST 2014

Hi Matt,

I'm afraid your options are somewhat limited here. The custom caches, as
you suspected, are just for gene and transcript data.

You can use the --custom flag to look for overlaps with your features in a
gff or similar (
http://www.ensembl.org/info/docs/tools/vep/script/vep_custom.html), but
this won't do any sequence-based analysis.

I could see two possible routes:

1) Write a plugin to do the analysis. Without knowing the nature of your
data, it's hard for me to guess at what you might have to do in the plugin,
but I anticipate you'd probably read features from a tabix-indexed data
file and then proceed with the analysis from there. The dbNSFP and CADD
plugins do similar things (https://github.com/ensembl-variation/VEP_plugins)

2) Add your data to a custom Ensembl Funcgen database, and either use this
directly or build a cache from it. I have no sense of how hard or easy this
might be; our Funcgen team might be able to give some insight here.


Will McLaren
Ensembl Variation

On 8 October 2014 19:56, Matt Wood <matt.wood at codifiedgenomics.com> wrote:

> We have some custom motifs and transcription factor binding sites that
> we'd like to get incorporated into our VEP output. I know that we can
> create custom caches, but that doesn't sound right for motifs. I know
> plugins are also a possibility.
> Do you have any suggestions about how I'd incorporate this into VEP or how
> I should get started?
> Thank you.
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