[ensembl-dev] DNV annotation problem?

[Sarah Hunt]

Dear Ken,

When a variant is described on the negative strand, we expect the
allele strings to be reverse complimented, so would expect the
reference allele for 140453136 - 140453137 to be GT. At the codon
level this gives GTg/AAg => V/K.

The input you supplied describes the reference as TG - at the codon
level this gives TGg/AAg which is why you are seeing the output of
W/K.


Best wishes,

Sarah

On Thu, Jan 16, 2014 at 9:28 PM, Chen,Ken <KChen3 at mdanderson.org> wrote:
> Dear VEP developers,
>
> First of all, thank you for offering this wonderful resource.  We really appreciate it.
> In our analysis, we found this DNV (hg19, negative strand) in BRAF
> 7       140453136       140453137       TG      AA
>
> The correct HGVS annotation should be BRAF.V600K
>
> However, VEP returned BRAF.W600K
>
> It is important for us to fix this problem but we analyze data from real patient.
> Please let us know how to do it.
> Thanks.
>
> -Ken
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