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Hello,<br>
<br>
I'm developing a plugin for VEP that calculates 5' & 3' flanking
sequence for each rs.<br>
<br>
I've the plugin 95% completed. I'm just missing how are rs IDs
called on VEP.<br>
Looking into Enseml Variation API I've found this:
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<a
href="http://www.ensembl.org/info/docs/Doxygen/variation-api/classBio_1_1EnsEMBL_1_1Variation_1_1VariationFeature.html">http://www.ensembl.org/info/docs/Doxygen/variation-api/classBio_1_1EnsEMBL_1_1Variation_1_1VariationFeature.html</a><br>
<br>
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.<br>
<br>
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.<br>
<br>
Plugin code can be found in Github:
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<a
href="https://github.com/guillermomarco/vcf_input/blob/master/flanking_sequence.pm">https://github.com/guillermomarco/vcf_input/blob/master/flanking_sequence.pm</a><br>
<br>
<br>
<br>
<br>
Thank you !<br>
<br>
Best regards,<br>
Guillermo.<br>
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