[ensembl-dev] Wrong ancestral allele?

[Anja Thormann]

Hi Fin,

that’s correct. In order to get the reference allele you need to parse the allele_string field. The reference allele is listed first.

Anja

> On 26 Jul 2018, at 11:08, Fin Swimmer <ensembl at need-login.de> wrote:
> 
> Hello Anja,
> 
> thanks for your quick reply. Good to know, I haved read "ancestral" as "reference allele".
> 
> So to get the reference allele using variation endpoint of the REST-API I have to parse "allele_string"? Or are there other ways?
> 
> fin swimmer
> 
> Am 2018-07-26 11:55, schrieb Anja Thormann:
>> Hi,
>> most other primates have an A at that genomic location:
>> http://www.ensembl.org/Homo_sapiens/Variation/Compara_Alignments?align=1141&db=core&r=7%3A117591144-117592144&v=rs184957926&vdb=variation&vf=39493132
>> [1]
>> HTH,
>> Anja
>>> On 26 Jul 2018, at 10:52, Fin Swimmer <ensembl at need-login.de> wrote:
>>> Hello,
>>> why is the ancestral allel for rs184957926 reported as A not as C?
>>> See:
>> http://www.ensembl.org/Homo_sapiens/Variation/Population?r=7:117591144-117592144;v=rs184957926;vdb=variation;vf=39493132
>>> fin swimmer
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>> Links:
>> ------
>> [1]
>> http://www.ensembl.org/Homo_sapiens/Variation/Compara_Alignments?align=1141&db=core&r=7:117591144-117592144&v=rs184957926&vdb=variation&vf=39493132
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