[ensembl-dev] VEP using CADD plugin for indels

Kirsley CHENNEN kchennen at unistra.fr
Fri Apr 17 16:21:22 BST 2015


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 
> <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,
>     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
>>     <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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