[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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