Hi, I studied the frequency of three SNPs located on X chromosome in a sample of in male and female subjects. Since males have one X chromosome, determining the allele of each SNP will consequentially give you the haplotype on the X chromosome. But in females, how can I determine the haplotype or the phasing ( ie which allele falls on which chromosome) ?

for example :

if for female 1 in my sample the genotype for my three SNPs where:

SNP 1: TA

SNP 2: CT

SNP 3: GA

so how can I be sure that the haplotype is TCG/ATA and not for example ACG/TTA ? or ATG/TCA?

I read in many articles about haplotype analysis software like haploview software

MLocus software

FAMHAP software

but all are not clear and there is no explanations.

I appreciate if you can explain the principle to me?