[ensembl-dev] VEP using CADD plugin for indels

[Will McLaren]

Hi Kirsley,

The dbscSNV data works slightly differently than the dbNSFP data; I've
added a separate plugin for this.

https://github.com/ensembl-variation/VEP_plugins/blob/master/dbscSNV.pm

Note the different process for tabix-indexing the data file.

Regards

Will



On 8 April 2015 at 23:22, Kirsley Chennen <kchennen at unistra.fr> wrote:

>  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,
> Kirsley
>
>
>
>
> 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 [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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