I downloaded the HapMap LD files, and am generating SNP data based on MAFs.
In order to complement the generated SNPs, I'm using the LDs. So now I have a list of SNPs for which HapMap has information on LD, LOD and D-prime. But not all values in these files appear helpful, for instance when LOD is <1 - no negative values in dataset).
I need a set of parameters to decide which LDs to use, and which to ignore.
Does anybody know whether there as consensuses on cut-off values for these variables?