[ensembl-dev] Complex variant issue

[Konrad Karczewski]

Ah great, I wasn't using any --pick's but the update to v77 seems to have solved this.




Thanks!


-Konrad

On Fri, Oct 31, 2014 at 5:28 AM, Will McLaren <wm2 at ebi.ac.uk> wrote:

> 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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