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

[Andrew Parton]

Hi Matt, 

Upstream/Downstream consequences should be reported on the occasions where a variant is found to be 5’/3’ of a gene - it shouldn’t depend on surrounding variants within the VCF. Could you please send me an example so that I can reproduce it and take a closer look?

Thanks,
Andrew

> On 11 Jan 2019, at 17:12, Matt Wood <matt.wood at codifiedgenomics.com> wrote:
> 
> 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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