[ensembl-dev] VEP using CADD plugin for indels

[Kirsley CHENNEN]

Hi again Will,
             I have a l'll question concerning dbNSFP data. With the 
latest release (dbNSFP3.0b2a, dbscSNV), by default the tabix indexing is 
on the hg38 coordinates, but if I want to use hg19 coordinates, will the 
following tabix indexing work?

tabix -s 1 -b 9 -e 9 dbNSFP.gz

Columns of dbNSFP_variant:
     chr: chromosome number
     pos(1-based): physical position on the chromosome as to hg38 
(1-based coordinate).
         For mitochondrial SNV, this position refers to the rCRS 
(GenBank: NC_012920).
     ref: reference nucleotide allele (as on the + strand)
     alt: alternative nucleotide allele (as on the + strand)
     aaref: reference amino acid
         "." if the variant is a splicing site SNP (2bp on each end of 
an intron)
     aaalt: alternative amino acid
         "." if the variant is a splicing site SNP (2bp on each end of 
an intron)
     rs_dbSNP142: rs number from dbSNP 142
     hg19_chr: chromosome as to hg19, "." means missing
     hg19_pos(1-based): physical position on the chromosome as to hg19 
(1-based coordinate).
         For mitochondrial SNV, this position refers to a YRI sequence 
(GenBank: AF347015)
     .
     .
     .

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
>>
>>
>
>

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mail.ensembl.org/pipermail/dev_ensembl.org/attachments/20150417/83222932/attachment.html>