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

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

gwas imputation plink
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written by mandar.bobade60 • mandar.bobade60

You can use beagle or remove triallelic SNPs from analysis.

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written by Fabio Marroni Fabio Marroni

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