Identify haplotype block using unphased genotype data

Question

[slykuaias]

I have some SNP array data of non-model species. I want to identify haplotype blocks using Hapview, I read think it can work with unphased genotype data but I want to know what is the theory behind that?

How to identify haplotype blocks if it is unphased genotype data?

And how did the software calculate confidence interval of D' ? I know how to calculate D' but how to calculate it's confidence interval?

Answer 1

[Zev.Kronenberg]

You have to know the phase of the genotypes before you can calculate anything regarding linkage or haplotype structure.

[Adrian Pelin]

Is it possible to calculate r^2 based on differences in allele frequencies among different samples? Without having any phased data that is.

[Zev.Kronenberg]

You can measure autocorrelation, but that is about it. An alternative is to find blocks of homozygosity via a hidden markov model.