[ensembl-dev] Allele_num = "?"
konradk at broadinstitute.org
Thu Jul 16 12:55:52 BST 2015
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!)
> 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.
> 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.
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