Deleted:Haploview LD output as an input for PLINK SNP pruning

Question

[Dhana]

Hi,

I did LD analysis using Haploview and have saved the results. The result of the LD file from Haploview is of the following format;

L1 L2 D' LOD r² CIlow CIhi Dist T-Int

I have quite a large number of pairwise LD values and also quite a large number of SNPs in haplotype blocks. I filtered them based on r² value greater than 0.5 but still the number is too huge. I would like to use PLINK to prune pairwise LD's to a manageable number. PLINK requires bed file as an input, anyone has suggestions on how to go about this. Since PLINK has options to convert VCF files to Haploview inputs is there a way to convert Haploview output to be used as an input for PLINK? Also any other suggestions for LD pruning are welcome.