Can Allele specific mapping handle polyploids?

[Adamtaranto]

Is it possible to make an allele-specific map with for genomes with ploidy > 2?

[nservant]

I do not think that the ploidy is an issue. However, it can only handle two alleles so far, is that your point ?

[ifoo1213]

I am guessing this question is about how to remove the multiple mapping pairs and only keep the unique mapping reads?