Question: Identify haplotype block using unphased genotype data
gravatar for slykuaias
3.9 years ago by
United States
slykuaias0 wrote:

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?


chip-seq • 1.6k views
ADD COMMENTlink modified 3.9 years ago by Zev.Kronenberg11k • written 3.9 years ago by slykuaias0
gravatar for Zev.Kronenberg
3.9 years ago by
United States
Zev.Kronenberg11k wrote:

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

ADD COMMENTlink written 3.9 years ago by Zev.Kronenberg11k

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

ADD REPLYlink written 3.8 years ago by Adrian Pelin2.1k

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

ADD REPLYlink written 3.8 years ago by Zev.Kronenberg11k
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