[ensembl-dev] Plugin behavior with SVTYPE
konradk at broadinstitute.org
Mon Jul 13 12:26:51 BST 2015
Hi Will/VEP team,
Me again with another VEP edge case (in both v79 and v80). When I go to annotate the following variant (and run plugins such as LOFTEE), it runs fine and returns information from the plugin.
chr1 20680261 . GCTGGCCTCCGGAGC G . PASS AC=1;AF=0.500;AN=2
However, when the record contains structural variant information (I think this was generated by Pindel), VEP runs fine but instead of the usual `-` for Allele, annotates it with `deletion` (this is fine), but then doesn't run any plugins on it.
chr1 20680261 . GCTGGCCTCCGGAGC G . PASS AC=1;AF=0.500;AN=2;END=20680275;HOMLEN=2;HOMSEQ=CT;SVLEN=-14;SVTYPE=DEL
Is this expected/is there a way around it?
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