[ensembl-dev] VEP using CADD plugin for indels
wm2 at ebi.ac.uk
Tue Apr 14 16:18:33 BST 2015
The dbscSNV data works slightly differently than the dbNSFP data; I've
added a separate plugin for this.
Note the different process for tabix-indexing the data file.
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,
> On 08/04/2015 14:51, Will McLaren wrote:
> 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
> Hopefully this should work for you
> Will McLaren
> Ensembl Variation
> On 3 April 2015 at 10:32, Kirsley CHENNEN <kchennen at unistra.fr> wrote:
>> 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?
>> Kirsley Chennen
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