Dear colleagues
I need your full help to provide me the equation, method ,software to calculate the haplotype of SNPs .. note that I have 88 patients I need to calculate their SNP haplotype
so please I urgently assist me with your full information
Best regards
Meelad
Dear Meelad,
Haplotype diversity is a measure of the uniqueness of a particular haplotype in a given population. The haplotype diversity (H) is computed as:
H = N/N+1 (1-Sigma xi2)
where Xi is the (relative) haplotype frequency of each haplotype in the sample and N is the sample size. Haplotype diversity is given for each sample.
For more details, please use the following link:
https://en.wikipedia.org/wiki/Haplotype
For programs dealing with this topic, please use the following link:
http://pngu.mgh.harvard.edu/~purcell/plink/ld.shtml
Hoping this will be helpful,
Rafik
Dear Rafik
I 'm very grateful for your help ; but unfortunately i'm incapable of calculating the haplotype from SNPs and the equation above I couldn't understand it or apply it anymore..so will you please if that doesn't bother you explain how the haplotype will be elicited from genotypes of SNPs???
Feeling so grateful if you do so..
Meelad
Dear Meelad,
First of all, you should start from Clark's algorithm and after understanding it, start inferring haplotypes for a few SNPs on a piece of paper.
Btw, how many SNPs have you typed?
If your SNPs are common and you have many of them, then I suggest using PHASE.
Hope it helps
Naser
http://stephenslab.uchicago.edu/software.html#phase
Dear Naser
So thankful for your precious advice I am going to read these methods profoundly and make true trials hopefully they will resolve my problem of calculating haplotypes from genotypes which are so many.
Kind regards
Meelad
Dear Sophie
Dear Ann
Thanks so much for your interest, unfortunately I have only a little information about bioinformatics and the softwares you mentioned above I do not know how to apply them to my SNP genotypes in order to elicit haplotypes .
The 88 samples are only for screening the genotypes in a small population and of course this may not give enough picture for the real population.
Carefully read...
starting from Table 3: Example Hardy–Weinberg principle calculation
https://en.wikipedia.org/wiki/Hardy%E2%80%93Weinberg_principle
p= frequency of haplotype"A"
q=frequency of haplotype"a"
Calculate your own data. If you fail, give your own data to calculate the frequency of haplotype.
https://en.wikipedia.org/wiki/Hardy%E2%80%93Weinberg_principle
Dear Shahnaij
thanks for interest..
I have recently downloaded the HaploView program to estimate haplotype frequencies ; but I am really facing problems with interpreting results!!
Best wishes
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