readytogo Posted March 17, 2011 Share Posted March 17, 2011 Hi, I have a bunch of genotype data (14 mutations and 312 samples). I have inferred the haplotypes (total of fifteen different haplotypes) and identified that there is LD between three pairs of SNPs. I have done all this using Arlequin and Phase software. What I need to do is identify if any of these haplotypes are the result of recombination. I understand that LD is eroded by recombination but I am just confused by the whole concept. I even get confused with the four gamete test! Can anyone help me with this? I can give more info if needed - i think I have just totally confused myself and I cant find any software that identifies the haplotypes produced by recombination (I have alot more data and will eventually be doing whole gene haplotypes for 60 mutations so I need to get to grips with this now!) Please help! Thanks x Link to comment Share on other sites More sharing options...
readytogo Posted May 6, 2011 Author Share Posted May 6, 2011 Does anyone fancy helping me out with this? I just want to know how to identify recombinant haplotypes...or how to do the four gamete test between pairs of mutations when I have 14 mutations. Help! Link to comment Share on other sites More sharing options...
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