[ensembl-dev] ALLELE_NUM issue

[Konrad Karczewski]

Hi Will, Ensembl/VEP folk,

I'm getting a weird multi-allelic issue in VEP v81 - when I annotate the below VCF, all annotations for the first site get an ALLELE_NUM of 2, which results in G->C being annotated as a frameshift (works fine when the SNV is on its own). Any ideas why this might be happening?

-Konrad

##fileformat=VCFv4.1
#CHROM  POS     ID      REF     ALT     QUAL    FILTER  INFO    FORMAT
1	898175	.	G	GC,C	.	.	.	.
1	898175	.	G	C	.	.	.	.
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