[ensembl-dev] Plugin behavior with SVTYPE

Will McLaren wm2 at ebi.ac.uk
Mon Jul 13 13:25:15 BST 2015

Hi Konrad,

VEP treats short variants and structural variants (SVs) differently - SVs
are analysed without considering sequence, and have a different object type
in the API (StructuralVariationFeature vs VariationFeature for short
variants). The VEP parser's flag for processing something as an SV is the
SVTYPE key in the VCF info field, so this is why they are being treated as

Without a patch to the code, the only way to avoid this would be to
remove/replace the SVTYPE key from the VCF.

Plugins can be configured to run on StructuralVariationFeatures; you would
need to add a method variant_feature_types to tell the plugin it can
analyse them. However, even with this the StructuralVariationFeature object
does not carry sequence or allele information, so probably something like
LOFTEE won't work:

sub variant_feature_types {
  # BaseVariationFeature is the parent class of VariationFeature and
  return ['BaseVariationFeature'];



On 13 July 2015 at 12:26, Konrad Karczewski <konradk at broadinstitute.org>

> 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
> Is this expected/is there a way around it?
> Thanks!
> -Konrad
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