[ensembl-dev] VEP Flanking sequence plugin

[Will McLaren]

Hello,

A variation feature object is created by the VEP to represent each
line of your input. If you don't give it a name in your input, then
the VEP constructs a name from the coordinates, which is what you are
seeing. Names can be added for variants in the third column (VCF) or
sixth column (tab-delimited input).

If you want the rsID of any existing variants that overlap yours, you
must run the VEP with the --check_existing flag; you will then find a
simplified hash representing each overlapping variant in the array
@{$vf->{existing}} (where $vf = $tva->variation_feature).

If you are looking for the original flanking sequence submitted with
the existing variant to dbSNP, then we don't store this in the
database. However, if you just want to retrieve the reference sequence
either side of your variant, that is easily done by getting and
expanding the feature slice attached to the variant (here I'm getting
100bp either side):

my $five_prime_seq = $vf->feature_Slice->expand(100, -1)->seq;
my $three_prime_seq = $vf->feature_Slice->expand(-1, 100)->seq;

Regards

Will




On 24 April 2013 09:13, Guillermo Marco Puche
<guillermo.marco at sistemasgenomicos.com> wrote:
> Hello,
>
> I updated the code in my git repo, and I still can't make it
> work:https://github.com/guillermomarco/vcf_input/blob/master/flanking_sequence.pm
>
> I still don't get why this is returning a string of type 1_41304886_C/T and
> not the rsID.
>
> $tva->variation_feature->variation_name;
>
>
> Thank you.
>
> Best regards,
> Guillermo.
>
>
> On 04/23/13 16:45, Guillermo Marco Puche wrote:
>
> Hello,
>
> I'm developing a plugin for VEP that calculates 5' & 3' flanking sequence
> for each rs.
>
> I've the plugin 95% completed. I'm just missing how are rs IDs called on
> VEP.
> Looking into Enseml Variation API I've found this:
> http://www.ensembl.org/info/docs/Doxygen/variation-api/classBio_1_1EnsEMBL_1_1Variation_1_1VariationFeature.html
>
> It seems that I need VariationFeature adaptor set so I can call
> "variation_name" method get the rs and then call "five_prime_flanking_seq" &
> "three_prime_flanking_seq" methods to get the flanking sequence.
>
> I don't know why even after changing adaptor I'm still getting
> "2_26739423_T/C" if I'm not using TranscriptVariation adaptor but
> VariantFeature I should be getting rsxxxxxx ID.
>
> Plugin code can be found in Github:
> https://github.com/guillermomarco/vcf_input/blob/master/flanking_sequence.pm
>
>
>
>
> Thank you !
>
> Best regards,
> Guillermo.
>
>
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