[ensembl-dev] VEP cannot annotate * alternate alleles

[Will McLaren]

Hi Konrad,

Thanks, this is fixed on 82.

I can push to 81 too if you need?

Will

On 17 November 2015 at 01:42, Konrad Karczewski <konradk at broadinstitute.org>
wrote:

> Hi Will,
>
> Along these lines, however, VEP doesn't seem to be writing ALLELE_NUM
> properly on these lines (particularly when the * is not last in the list).
>
> For instance, when annotating this (VEP v81 and 82):
>
> 1       874817  rs201898716     C       *,T
>
> it gives the same output as if the ALT were T,*
>
> Hope it's an easy fix!
> -Konrad
>
> On Nov 16, 2015, at 12:36 PM, JESSICA X. CHONG <jxchong at uw.edu> wrote:
>
> Ahhh ok, this makes sense to find the annotation on the previous line.
>
> Thanks.
>
> On Nov 16, 2015, at 3:00 AM, Will McLaren <wm2 at ebi.ac.uk> wrote:
>
> Hi Jessica,
>
> The * allele is not annotated because there is nothing to annotate; it
> represents the absence of any allele due to an upstream deletion. The
> upstream deletion will of course be annotated.
>
> Example:
>
> REF:  ACGGTAGC
> S1 :  ACG----C
> S2 :  ACGGCAGC
>
> There are two mutations here; one deletion in S1, and one SNP in S2.
> Because the sequence containing the SNP is absent in S1, the genotype calls
> for this site in individuals with the deletion are otherwise impossible to
> annotate, unless you use the * notation.
>
> So the VCF looks like this:
>
> chr1 3 GGTAG G   ... 1/1 0/0
> chr1 5 T     C,* ... 2,2 1/1
>
> VEP will annotate the deletion as normal, but will only annotate the C ALT
> allele for the SNP; the * represents the absence of an allele, so no
> annotation is added - the deleted sequence is annotated for the variant on
> the previous line.
>
> Hopefully that makes sense!
>
> If you can provide an example of where you think VEP is doing something
> wrong then of course please do let us know.
>
> Regards
>
> Will McLaren
> Ensembl Variation
>
> On 13 November 2015 at 21:35, JESSICA X. CHONG <jxchong at uw.edu> wrote:
>
>>
>> http://gatkforums.broadinstitute.org/discussion/6240/what-means-is-in-alternative-allele
>>
>> Apparently GATK now uses * to represent long “upstream deletions.”
>>
>> It looks like as of v82, VEP cannot handle annotation of * alleles. The
>> lines in the resulting VCF completely lack VEP’s CSQ field.
>>
>>
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