How to harmonise target SNPs and proxy SNPs?

[zhuziwei5225]

Hello,
I found proxy SNPs with vcftools. How can I correct the beta when the alleles of target SNP and proxy SNP do not correspond for the same SNP? harmonise_data() will remove the ambigous SNP.
For example:
exposure effect of target SNP =0.5
effect allele = A
other allele = T

outcome effect of proxy SNP =-0.05
effect allele = A
other allele = C

or

exposure effect of target SNP =0.5
effect allele = A
other allele = G

outcome effect of proxy SNP =-0.05
effect allele = A
other allele = C

Thank you.

[wangyiyisheng]

Have you addressed this problem?