Biallelic SNPs in Tetraploids via the UNEAK pipeline

[KemKa]

Hello,

currently I am working on a supposed autotetraploid plant without a reference genome. We got data from Illumina sequencing and did SNP calling via the Tassel UNEAK pipeline.
Now I come to my question, why are all the SNPs we got from the pipeline bi-allelic? I would suppose that I could also have triallelic or even tetraallelic SNPs in a tetraploid plant. Maybe it`s a stupid question but I`m new in this field and I`m the only one in our group working on tetraploids.

I would be glad if somebody could answer my question
Thank you in advance

[luc]

I am not familiar with Tassel; I assume though that triallelelic SNPs are so rare that they do not warrant the effort to accommodate them bioinformaticaly.