How To Do Imputation For File Which Possesses Markers More Than 2 Alleles

Question

[mandar.bobade60]

Hi all,

I am doing imputation for GWAS with MACH but every time it is giving problem:

FATAL ERROR: This version of MaCH is designed for bi-allelic markers However, the following marker(s) have >2 alleles:

What is the way out from this?

Is plink imputation efficient? However, I have found out in >2 alleles beagle is the only option. Please guide me how I can proceed from this.

Thanks in advance,

MANDAR

[Fabio Marroni]

You can use beagle or remove triallelic SNPs from analysis.