[ensembl-dev] Allele_num = "?"

[Konrad Karczewski]

Hi Will,

That seems to have fixed a bit (gets through the variant I mentioned before), but still adds ?'s to:

1    224102777       .       CTTTTTTTTTTTT   CTTTTTTTTTTTTTTTT,CTTTTTTTTTTTTTT,CTTTTTTTTTTTTTTT,CTTTTTTTTTTTTTTTTTT,CTTTTTTTTTTTTT,C

(Horrifying variant, I know, but does come up!)

Thanks!
-Konrad

> On Jul 8, 2015, at 10:38 AM, Will McLaren <wm2 at ebi.ac.uk> wrote:
> 
> Hi Konrad,
> 
> Thanks, this is a bug when using --minimal. This is fixed on release/80 now.
> 
> Will
> 
> On 7 July 2015 at 14:51, Konrad Karczewski <konradk at broadinstitute.org <mailto:konradk at broadinstitute.org>> wrote:
> Hi Will/VEP team,
> 
> Found something unexpected when annotating ExAC with VEP v80. The following variant:
> 
> 1    139345  .       CGTT    C,TGTT
> 
> seems to annotate without error/warnings, but for some of the entries, ALLELE_NUM is `?` - the first few I checked seem to be upstream_gene_variant and the like, so I'm assuming maybe this means both alleles get the same annotation, but I can't find anything in the documentation.
> 
> Any information you might have would be very helpful.
> 
> Thanks!
> -Konrad
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