**20**wrote:

Is there a good way to take any two SNPs and pull out the LD between them, particularly the R-squared and **the directionality of the linkage (e.g. A in SNP1 occurs with G in SNP2 95% of the time)**?

Obviously I can do this manually, but I am wanting to do it for a list of several thousand SNPs, so I am hoping for a scalable solution. Right now I can't find anything, and it looks like I will have to come up with my own solution using `vcftools`

and the 1000 genomes data.

Thanks!

**2.2k**• written 4 days ago by Mike Dacre •

**20**

It turns out that LDLink does this beautifully for a single pair of rsids, but it doesn't seem to work in batch mode: https://analysistools.nci.nih.gov/LDlink/

20Maybe it's possible that you could get your results from LDlink with some scripting as well, possibly requires parsing the html for ex.you can construct URLs programmatically pretty easily https://analysistools.nci.nih.gov/LDlink/?var1=rs1042779&var2=rs6792369&pop=YRI%2BLWK%2BGWD%2BMSL%2BESN%2BASW%2BACB%2BMXL%2BPUR%2BCLM%2BPEL%2BCHB%2BJPT%2BCHS%2BCDX%2BKHV%2BCEU%2BTSI%2BFIN%2BGBR%2BIBS%2BGIH%2BPJL%2BBEB%2BSTU%2BITU&tab=ldpair

460Yes! It looks like that does work, I am not sure how many queries their API can tolerate, but I am going to try this tonight to see. I also want to compare this to running the calculations with plink/vcftools to see which is faster/more stable. Thanks!

20