chr1swallace
commented
4 years ago Dear Sergio,
the method is symmetric in MAF, 1-MAF, so you can go ahead and use EAF.
Chris
On 02/10/2020 11:08, Sergio Chavez wrote:
Dear reader,
I am trying to use coloc for the first time. I want to perform fine mapping and colocalization analysis between two traits. For one trait i only have the sum. stats from a meta analysis and for the other trait i have QTL info. For both traits, i have the EAF (instead of MAF), aan the beta refers to the Effect allele. My question is as follows: Should i use a beta that also refers to the minor allele, or is this not necessary? I ask this, because for some snps, the effect allele is not the minor allele, so, if i would like to report the beta for the minor allele, i would the have to change the direction.
Hope you can help me out.
thank you very much in advance,
Sergio
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schavezchavez
Dear reader,
I am trying to use coloc for the first time. I want to perform fine mapping and colocalization analysis between two traits. For one trait i only have the sum. stats from a meta analysis and for the other trait i have QTL info. For both traits, i have the EAF (instead of MAF), aan the beta refers to the Effect allele. My question is as follows: Should i use a beta that also refers to the minor allele, or is this not necessary? I ask this, because for some snps, the effect allele is not the minor allele, so, if i would like to report the beta for the minor allele, i would the have to change the direction.
Hope you can help me out.
thank you very much in advance,
Sergio