[ensembl-dev] VEP using CADD plugin for indels

Kirsley Chennen kchennen at unistra.fr
Wed Apr 8 23:22:17 BST 2015

Hi Will,
         Marvellous! Is it also possible to have an update of the 
dbNSFP.pm plugin, as 
dbNSFP[https://sites.google.com/site/jpopgen/dbNSFP] now comes in two 
files; dbNSFP.XXX.zip for non-synonymous SNPs and dbscSNV.zip for 
splicing consensus regions?
Thanks again.

Best regards,

On 08/04/2015 14:51, Will McLaren wrote:
> 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 <http://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 
> <mailto: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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