[ensembl-dev] VEP using CADD plugin for indels

[Will McLaren]

I've patched a fix to the plugin, please update and try it again.

Will

On 17 April 2015 at 16:21, Kirsley CHENNEN <kchennen at unistra.fr> wrote:

>  Hi,
>         Unfortunately, it seems that the dbscSNV.pm module have some bug.
> It detects the file, but do not extract the scores:
> - VEP v79 on genome version GRCh37
> >  echo "16 56548593 56548593 C/G" | ./variant_effect_predictor.pl
> --force_overwrite --database --port 3337 --dir_plugins ./cache/Plugins
> --plugin dbscSNV,./datasets/vep/dbNSFP/dbscSNV.txt.gz
>
> - It added the 'ada_score' and 'rf_score' in the header but did not
> extract any!
>
> - These coordinates are well in the file of dbscSNV.zip v1.0
> > zcat dbscSNV.txt.gz | grep --color -P '^16\t56548593\tC\tG'
> 16    56548593    C    G    y    y    splicing
> BBS2(NM_031885:exon3:c.118-1G>C)    .    .    splicing
> ENSG00000125124(ENST00000568104:exon3:c.118-1G>C;ENST00000245157:exon3:c.118-1G>C)
> .    .    0.999986675681007    0.932
>
> Could you help me with this issue please? Thanks.
>
> Regards,
> Kirsley
>
>
>
> 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.
>
>  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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