[ensembl-dev] Condel plugin in VEP

[Will McLaren]

Hello,

I think that this behaviour is a feature of Condel itself - there's no flag
you can set on the plugin to deal with these cases.

You could try editing the plugin yourself - there's an if() clause in the
run method that you'd need to edit, and you'd also need to change the logic
in the compute_condel() subroutine. I think there are some dangers here
though as PolyPhen's score for an unknown prediction is 0.

In my opinion you'd be safer just having the VEP report SIFT, PolyPhen and
Condel and taking into account all three.

Hope that helps

Will McLaren
Ensembl Variation


On 6 February 2014 17:35, Genomeo Dev <genomeodev at gmail.com> wrote:

> Using Condel plugin in VEP in Ensembl VM74
>
> Hi,
>
> Condel seems not predict if either Polyphen or SIFT predictions are not
> calculated or if Polyphen prediciton is returned as unknown(0).
>
> Is there a way to alter this behaviour to allow Condel to make a
> prediction even using one method? For example there are cases where there
> is severe impact predicted by SIFT, while Polyphen predicts it as unknown.
> Condel shows no prediction for that.
>
> Thanks,
>
> G.
>
> _______________________________________________
> Dev mailing list    Dev at ensembl.org
> Posting guidelines and subscribe/unsubscribe info:
> http://lists.ensembl.org/mailman/listinfo/dev
> Ensembl Blog: http://www.ensembl.info/
>
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mail.ensembl.org/pipermail/dev_ensembl.org/attachments/20140207/7d2c8dab/attachment.html>