Haploview VS plink for LD R2 caculating ,which is fast

[xujie]

Hi everyone .I am going to caculate the R2 for the LD estimating and the data is too big(1500,000 snps in a singal chromosome)
Haploview and Plink both can get the R2 but which one is more fasta for the big data?
Should I cut the big data into piceces when I doing the job? How can I set the standard for cutting?

Thank you

My best wishes

[jason.laramie]

Hi,
I would probably use plink and only calculate pairwise R^2 for SNPs that are within 5-10Mb of each other. This should capture most of the inherent LD structure and help you trim the list down of pairs of SNPs that will need to be computed.

Kind Regards,
Jason

[xujie]

Hi,
I would probably use plink and only calculate pairwise R^2 for SNPs that are within 5-10Mb of each other. This should capture most of the inherent LD structure and help you trim the list down of pairs of SNPs that will need to be computed.

Kind Regards,
Jason

Thank you very much