[ensembl-dev] VEP using CADD plugin for indels
kchennen at unistra.fr
Fri Apr 17 09:18:08 BST 2015
On 14/04/2015 17:18, Will McLaren wrote:
> Hi Kirsley,
> 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
> <mailto: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
>> 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
>> 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:
>> 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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