I am having this problem because I need to run a meta-analysis and to align
all the variants between the different studies included in the
meta-analysis I need to know the effect allele used to get the beta (so
that I can flip the beta if the effect allele is flipped compared to all
other studies).

Thanks for your help.

Francesca


2014-05-26 11:13 GMT+01:00 francesca casalino <francy.casalino@gmail.com>:

> But then how do you know which allele is the reference and which the risk
> allele (between A/T/C/G)?
>
>
> 2014-05-26 1:41 GMT+01:00 David Duffy <David.Duffy@qimr.edu.au>:
>
> francesca casalino <francy.casalino@gmail.com> asked:
>>
>>
>>> Does anyone know how to find the reference allele used for genetic
>>> associations ran in snpStats?
>>>
>>>  A is ref allele, B is risk allele.
>>
>>
>>
>>
>

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