[ensembl-dev] VEP ClinVar information

[Will McLaren]

If you enable the --check_existing flag when you run the VEP, you'll be
able to see any known co-located variants attached to the VariationFeature
object in your plugin:

sub run {
  my $self = shift;
  my $tva = shift;
  my $vf = $tva->variation_feature;

  foreach my $known_var(@{$vf->{existing} || []}) {
     # do stuff
  }
}

The $known_var is not an API object but a simple hashref with a number of
fields; you're probably interested in $known_var->{clin_sig}

However, as I mentioned, this is the only data that is stored in the cache.
To access the rating and the specific disease association, you'll need to
make calls to the database by getting an adaptor, something like:

sub run {
  my $self = shift;
  my $tva = shift;
  my $vf = $tva->variation_feature;
  my $pfa =
$self->{config}->{reg}->get_adaptor('human','variation','phenotypefeature');

  foreach my $known_var(@{$vf->{existing} || []}) {
     foreach my
$pf(@{$pfa->fetch_all_by_object_id($known_var->{variation_name})}) {
       # do stuff
     }
  }
}

Be aware that this will access the database, so unless you have a local
copy please don't run this sort of code on genome-wide VCFs using our
public DB server.

Regards

Will

On 2 March 2015 at 14:47, Guillermo Marco Puche <
guillermo.marco at sistemasgenomicos.com> wrote:

>  Hi Will,
>
> Indeed I'm looking to retrieve this information from VEP plugin.
>
> Regards,
> Guillermo.
>
>
> On 02/03/15 15:25, Will McLaren wrote:
>
> Hi Guillermo,
>
>  The detailed ClinVar information is stored against PhenotypeFeature
> objects (each SNP/disease pairing gets its own entry in ClinVar, e.g.
> http://www.ncbi.nlm.nih.gov/clinvar/RCV000019691.2,
> http://www.ncbi.nlm.nih.gov/clinvar/RCV000019692.2/,
> http://www.ncbi.nlm.nih.gov/clinvar/RCV000019693.2/ for rs699).
>
>  The rating (and indeed the clinical significance) is stored as an
> attribute on the PhenotypeFeature object; you can retrieve this with the
> get_all_attributes() method.
>
>  See
> http://www.ensembl.org/info/docs/Doxygen/variation-api/classBio_1_1EnsEMBL_1_1Variation_1_1PhenotypeFeature.html
> and
> http://www.ensembl.org/info/docs/api/variation/variation_tutorial.html#phenotype
> for more info.
>
>  Bio::EnsEMBL::Variation::Utils::VEP::get_clin_sig() is an internal
> method that you should not use.
>
>  The VEP cache contains the list of clinical significance states for each
> variant, but neither the disease association or the rating. If you want
> help getting access to this data via a plugin, let me know as it's a little
> more involved than the API methods above (though it is faster as no
> database access is required).
>
>  Regards
>
>  Will McLaren
> Ensembl Variation
>
> On 2 March 2015 at 14:06, Guillermo Marco Puche <
> guillermo.marco at sistemasgenomicos.com> wrote:
>
>>  Dear devs,
>>
>> I'm looking forward to retrieve ClinVar information and add it to VEP
>> annotation. From my understanding I should be able to retrieve "Clinical
>> significance" and "ClinVar Rating".
>>
>> I've been looking the Varation API, and I'm confused. I guess for
>> significance I should use
>> Bio::EnsEMBL::Variation::Utils::VEP::get_clin_sig() or
>> Bio::EnsEMBL::Variation::VariationFeature::get_all_clinical_significance_states().
>>
>> What about ClinVar rating? Is it possible to retrieve it from API?
>>
>> Thanks!
>>
>> Regards,
>> Guillermo.
>>
>>
>>
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>>
>
>
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>
> --
>  ------------------------------
>
> *Guillermo Marco Puche*
>
> Bioinformatician, Computer Science Engineer
> Sistemas Genómicos S.L.
> Phone: +34 902 364 669 (Ext.777)
> Fax: +34 902 364 670
> www.sistemasgenomicos.com
>
>  <https://www.sistemasgenomicos.com/web_sg/web/areas-bioinformatica.php>
>    ------------------------------
>
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