[ensembl-dev] Plugin behavior with SVTYPE

[Konrad Karczewski]

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?

Thanks!
-Konrad