I have a list of SNPs, and I want to find all SNPs in LD with them over a given threshold (D' > 0.99, LOD > 3). I've found tools to do this on the basis of the r2 value (eg HaploReg), but while these generally output the D' statistic, they omit the LOD value.
My current solution is to pull a region 200 kb either side of my tag SNP out of the 1000 Genome vcf files, filter the non-biallelic sites out and then look for all pairwise LD values using HaploView (which also outputs LOD). I then filter this output using the stated threshold.
This takes quite a long time to run, and while it's a workable solution when I'm just looking at a few tag SNPs, I'm going to be doing it on a much larger scale and so would prefer something a little more efficient.