[ensembl-dev] Complex variant issue

[Will McLaren]

Hi Konrad

Are you using one of the filtering flags (--pick, --per_gene etc)?

--pick chooses one consequence per input variant; you can use --pick_allele
to choose one consequence per input allele. If I do so I see
inframe_deletion and missense_variant:

CSQ=A|ENSG00000203782|ENST00000368742|Transcript|inframe_deletion|142-157|85-100|29-34|SGGGGC/S|AGCGGCGGTGGTGGCTgc/Agc|||1|LOR|HGNC|6663|protein_coding|YES|CCDS30870.1|ENSP00000357731|LORI_HUMAN|Q6FHY3_HUMAN|UPI0000470BBD|||2/2||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50315|ENST00000368742.3:c.85_100delAGCGGCGGTGGTGGCTinsA|ENSP00000357731.3:p.Gly30_Cys34del||||||||||||||,GGCGGCGGTGGTGGCT|ENSG00000203782|ENST00000368742|Transcript|missense_variant|142-157|85-100|29-34|SGGGGC/GGGGGC|AGCGGCGGTGGTGGCTgc/GGCGGCGGTGGTGGCTgc|||1|LOR|HGNC|6663|protein_coding|YES|CCDS30870.1|ENSP00000357731|LORI_HUMAN|Q6FHY3_HUMAN|UPI0000470BBD|||2/2||Low_complexity_(Seg):Seg&PROSITE_profiles:PS50315|ENST00000368742.3:c.85_100delAGCGGCGGTGGTGGCTinsGGCGGCGGTGGTGGCT|ENSP00000357731.3:p.Ser29Gly||||||||||||||

Let me know if you still don't see this (I tested using VEP 77).

Will

On 31 October 2014 05:29, Konrad Karczewski <konradk at broadinstitute.org>
wrote:

>   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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