Generating .bed file and .map file for polyploid vcf file through plink

Question

[analyst]

Dear all,

I need bed files for admixture and map files for beagle imputation for polyploid plant. I tried through Plink but it do not support polyploid organisms. If I use --allow-extra-chr flag to run it anyway, I observed 0s in third row of output .bim and .map file.

Your help will be highly appreciated.

Answer 1

[chrchang523]

Why do you think ADMIXTURE supports polyploid input? (Note that this is an answer, not a comment.)