I have the relative frequencies of the haplotypes for two loci A and B with two alleles each. Lately I have been struggling-
1. To estimate the haplotypes and
2. To calculate the LD between the two alleles
using the program "PHASE" , as the output makes no sense to me.
This is because I have never done such calculations prior and my present work requires that I analyze the haplotypes for association.
I would be really grateful if any one would help me with this analysis.
Thank you Mr Bhoom Suktitipal
I will check the same and revert back at the earliest.
Hi!
PHASE is a nice software and has the advantage to assign the pair of haplotypes to single samples, but has no graphic interface. Maybe the most used software is Haploview by the Broad Institute (http://www.broadinstitute.org/scientific-community/science/programs/medical-and-population-genetics/haploview/haploview). It has been adopted for the HapMap project, the project that studied the SNPs in different populations all over the world. It requires 2 simple input files and has a user-friendly interface. You have both a graphical and tabular output of LD (I suggest to use D') and performs association studies (both case-control and on trios). The instructions are brief and clear.
Good luck!
I agree that Haploview is more appropriate to use in your case.
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