Hello, I am working with polyploid plant species (tetraploid, hexaploid, octaploid). I have genotype by sequencing (GBS) SNP data from different sequencing platforms like Affymetrix and SeqSNP. Now, I want to perform SNP imputation for some species and increase the number of SNPs and also find overlapping SNPs from two different sequencing platforms. I do not have Map information but I do have a reference SNP dataset. I see that there are lots of tools like Beagle, Impute etc. to impute SNPs. But these tools are specifically used for diploid organisms.

Since I am working with polyploids, can anyone suggest me some tools for SNP imputation in polyploids?

Thank you.

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