Pairwise LD computation

[Joana Monteiro]

How do we calculate pairwise LD given that we have a list with the SNPs of interest for the ld computation? In this case, we don't want to compute the LD for SNPs that aren't within this list.

[Christopher Chang]

Is there a reason you can't just use --extract on your SNP list?

[Joana Monteiro]

Hi! Yes, that is what I will be doing most likely: --extract the SNPs of interest from the list and then for the LD computation window I will measure the lenght from the first SNP position to the last position and multiply it by 2 so there is room for the computation to be thorough. I asked this question in case there was a more direct approach to this problem that was already available.

[Joana Monteiro]

After doing all the steps I mentioned I found a problem in the output (.ld file). I had 27 SNPs of interest originally and I should have the 27 SNP pairs to which ld values are computed in the output for each SNP, but that doesn't happen, for each SNP I seem to be getting different numbers of SNP pairs and I don't understand why. I must add that what I did for testing purposes was to put a r2 threshold equal to zero so I would get all the pairs.

For example, I input the command:

> plink --bfile DATA --ld-window-kb 880000 --ld-window-r2 0 --r2 --ld-snp-list snp_list.txt --out testLD --allow-no-sex

And in the output file I found that it doesn't compare the rs71373525 with the rs11736137. Then I tried this command to see the r2 value for this specific pair:

> plink --bfile DATA --ld rs117326137 rs71373525 --allow-no-sex

This way the ld is computed just fine and it should pass the threshold of zero in the other command. Any suggestions on why this happens?

[Christopher Chang]

plink 1.x takes the *intersection* of the --ld-window and --ld-window-kb settings... and the default --ld-window setting is 10.  (Which was reasonable, in 2007.)  I'll be changing that default to "infinity" in plink 2.0, but until then, you need to add something like "--ld-window 880000" to your command line.

[Joana Monteiro]

Thank you Christopher! It works just fine now, thank you for the reply!