[ensembl-dev] Complex variant issue

[Konrad Karczewski]

Hi dev team,


Another one for you, this one possibly a bit more complicated. So recently, we've been seeing many more multi-allelic variants in VCFs of larger cohort sizes, some of which seem to be interfering with VEP a bit. For instance, this entry:


1       153233510       .       AGCGGCGGTGGTGGCT        GGCGGCGGTGGTGGCT,A



is printed as complex, but in reality, is an A->G (1st alt allele), and an indel (AGCGGCGGTGGTGGCT->A). VEP annotates the deletion as an inframe deletion (correctly - annotation below), but does not output anything for the A->G (which in reality is a missense variant).


CSQ=-|ENSG00000203782|ENST00000368742|Transcript|inframe_deletion|143-157|86-100|29-34|SGGGGC/S|aGCGGCGGTGGTGGCTgc/agc||||2|2/2|||||||1||YES|LOR|HGNC||||protein_coding|ENSP00000357731|Low_complexity_(Seg):Seg&PROSITE_profiles:PS50315|CCDS30870.1|ENST00000368742.3:c.86_100delGCGGCGGTGGTGGCT|ENSP00000357731.3:p.Gly30_Cys34del|||||||||




-Konrad
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