Hi Fatma!

You can use PLINK (it's free ) http://zzz.bwh.harvard.edu/plink/tutorial.shtml

You can use it to do an association test or a permutation test. It is useful to find loci associated with diseases. I think the PLINK is good for beginners.

Haplotype partition is useless if it is not connected to the meiotic process. Therefore for further research, I recommend you to use software for IBD mapping.

IBD segment is a haplotype partition shared by two or more individuals and inherited from a common ancestor (IDB segment connected to meiosis). Therefore IBD mapping is more informative and provides enough statistical power for a small sample. For IBD mapping we use the following soft: BEAGLE, DUSH, PLINK.

Workflow is following:

BEAGLE do haplotype phasing and pairwise IBD (hap. partitions);

(https://faculty.washington.edu/browning/beagle/beagle.html)

DUSH do multi-IBD;

(http://www1.cs.columbia.edu/~gusev/dash/)

PLINK do permutation test.

Last step (permutation test) shows IBD segments significantly associated with disease (see attached abstract). I can help you to do IBD mapping.

Best,

Ural

Thank you so much, Dr. Ural Yunusbaev for your answer and for recommending PLINK. I face a problem in installing PLINK on MacOS. Could PLINK work properly on MAC?

I think IDB is more related to family-based genetic association studies. My research is in haplotype block partitioning to determine which haplotype blocks are associated with a certain disease rather than individual SNPs. Haplotype block is more significant than individual SNPs. I found HapBlock software that uses dynamic programming algorithm for haplotype blocks partitioning but I failed to download it. It would be greatly appreciated if you could help me.

Kind regards and thanks in advance.

Fatma