how to identify haplotypes and its frequency based SNP genotyping data?

Question

[blacktomato27]

Hi to all good Evening i am new to identifying haplotypes and analysis based on haplotypes. Now i have SNP genotyping data on my 150 lines with 3000 snps in this format.

SNP alleles chrom Pos IND1 IND2 IND3 IND4 IND5

SNP1 A/G 6 27936 AA AA AA AA AA

SNP2 T/C 6 37057 TT TT TT TT TT

SNP3 A/G 6 60790 AA AA AA AA AA

SNP4 C/T 6 79641 CC CC CC CC CC

Now i would like to haplotypes from the above data. i would like to request you all to share your expertise in this analysis like any softwares, R packages etc to do this analysis. any help in this regard will be highly appreciated Regards

[curious]

like a haplotype defined by multiple snps? I would imagine you have to code that up in R yourself.

Answer 1

[Kevin Blighe]

Going the PLINK / HaploView route would be among the primary ways to do this:

• How do I compute ld blocks from the hapmap ld_data?
• How to draw LDheapmap using plink.ld result

In R, I am not sure. SNPRelate, a common package, does not seem to have functionality for identifying haplo-blocks and -types.

Kevin