Imputation for haploid organisms

[adomron24]

Hello,

I would like to use bigsnpr to compare the output of clumping vs pruning in my snps dataset from Zymoseptoria tritici. As it is an haploid organism, and I have selected only bialellic snps, I only have 0 (reference) or 2 (alternate) values for my variants after converting the .bed file from plink to bigsnp object.

However, when I try to impute the missing values I end up having "1" values, which would be incorrect since no heterozygous variants should be found. Is there any additional parameter recommended to fix this?

Thank you,

Alex

[privefl]

• Which function are you using for imputation?
• What's the typical proportion of missing values per variant you have?

[privefl]

Any update on this?