[ensembl-dev] upstream/downstream changes based on context in vcf?

[Matt Wood]

I was hoping to get some clarification on how the upstream_gene_variant and
downstream_gene_variant consequences are determined.

We've found several cases where a variant will have downstream or upstream
consequences when that variant appears in one VCF, but will be annotated
without those consequences when in another VCF.

Our best guess is that the context of surrounding variants in the VCF is
changing whether those consequences are applied.

Is that how it is supposed to work? We're running version 89.7.

Matt
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