[ensembl-dev] VEP using CADD plugin for indels

[Will McLaren]

Hello,

Looking at the CADD website, it seems the data files for indels are
separate from those for SNVs.

I've updated the CADD plugin (
https://github.com/ensembl-variation/VEP_plugins/blob/master/CADD.pm) to be
able to run with more than one CADD data file specified, e.g.:

perl variant_effect_predictor.pl [your_options] -plugin
CADD,whole_genome_SNVs.tsv.gz,InDels.tsv.gz

Hopefully this should work for you

Will McLaren
Ensembl Variation

On 3 April 2015 at 10:32, Kirsley CHENNEN <kchennen at unistra.fr> wrote:

> Hi,
>     I would like to know how to use the CADD plugin with VEP to annotate
> both SNP and indels? In the plugin head description, it seems to refer only
> to SNP. Is there a way to annotate the indels too?
>
>
> Regards,
> Kirsley Chennen
>
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