SNP studies (Haplotype analysis) - (Mar/20/2006 )
I am presently working out the role of SNPs associated to one of the diseases and have come up with some promising leads. Now the problem lies with the haplotype analysis. I would be grateful if you could please guide for how to do the same and if there is any online software available in order to save my time.
Can you give some more details about what do you want to do? If you need to resolve the haplotypes, you should be using PHASE- a program that infers the haplotypes from diploid sequence data.
Once you have done that,what association test you need to use depends on what type of population and genotype data you have. A few options for association testing are FBAT, QTDT or TASSEL...