[ensembl-dev] VEP cannot annotate * alternate alleles

[Will McLaren]

Done - only slightly annoying :-)

Will

On 18 November 2015 at 15:15, Konrad Karczewski <konradk at broadinstitute.org>
wrote:

> Hi Will,
>
> Thanks! If it's not too much trouble to push to 81, that'd be great (I
> haven't tested 82 too much yet). If it's annoying though, don't worry about
> it.
>
> Thanks!
>
> -Konrad
>
>
> On Wed, Nov 18, 2015 at 8:18 AM, Will McLaren <wm2 at ebi.ac.uk> wrote:
>
>> 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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>>
>
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