[ensembl-dev] VEP using CADD plugin for indels

[Will McLaren]

Hello,

Yes, I believe this should work.

Will

On 17 April 2015 at 09:41, Kirsley CHENNEN <kchennen at unistra.fr> wrote:

>  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> 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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