variant prioritization in variants table

[matthdsm]

Hi Brent,

Could you explain the logic of how gets decided which variant/transcript makes it into the variants table? My understanding was that the variant with the most severe consequence gets added to the variants table, while other transcripts are relegated to the variant_impacts table. Is this correct?

We have a sample in which we've a identified a variant with multiple consequences, of which some are of HIGH impact. The transcript in the variants table only refers to a MEDIUM impacts.

I've created a gist with the variant in question. Could you have a look and let me know if this behavior is expected?

The VCF was created through bcbio. Relevant software versions:

ensembl-vep               90.3                htslib1.5_0    bioconda
vcf2db                    2017.04.12               py27_0    bioconda
geneimpacts               0.3.3                    py27_0    bioconda

Thanks M