[ensembl-dev] VEP Flanking sequence plugin
Guillermo Marco Puche
guillermo.marco at sistemasgenomicos.com
Tue Apr 23 15:45:21 BST 2013
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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