Hello all,

   I was a little confused by this plink output im producing. It was my understanding that --indep-pairwise analysis using a cutoff value for r2 would identify all the SNPs in a .ped file with an r2 correlation value of >.7 

    $ ./plink --file input.plink --indep-pairwise 225 23 .7 --out plinkoutput1 

SNPs with a r2 >.7 would have their IDs saved to a file 'prune.in' while those with a r2 < .7 would be saved to a second file called 'prune.out'. Now, if you want to get the tagging SNPs and a list of all the SNPs they tag, you run something along the lines of 

    $ plink --file input.plink --show-tags my_tags.txt --list-all --tag-r2 .7 --out mytags_and_what_they_tag

So it makes sense that you could use the prune.in list of SNPs for the list of tags right?

    $ plink --file input.plink --show-tags input.prune.in --list-all --tag-r2 .7 --out mytags_and_what_they_tag

and in the output every SNP should appear as either a tag for something, or something that is being tagged by another snp. But when I look at the file:

        SNP  CHR         BP NTAG       LEFT      RIGHT   KBSPAN TAGS
     rs79687004    2    5501148    0    5501148    5501148        0 NONE
      rs1404257    2    5503200    1    5498227    5503200    4.973 rs10929518
     rs61268182    2    5504924    2    5491746    5504924   13.178 rs72776977|rs955146
     rs17356301    2    5506274    0    5506274    5506274        0 NONE

  I see things like rs79687004. In its 'TAGS' column it has NONE. So its not serving as a tagging SNP for anything. Fair enough, but when I search for it in the file this is the ONLY instance of 'rs79687004'. Its not being listed in some other SNP's TAGS column either. Heres where I am confused: if everything in prune.in is a SNP that correlated to something else at an r2 > .7, wouldnt every single SNP either be identified as tagging something or tagged by something in this output? Ie shouldnt a SNP that is not tagging anything, in addition to having its on line in the output ALSO appear in some other line as a tagged SNP? 

The only thing I can think as an explanation is that my scanning window used during --pairwise-indep was 225 SNPs, and this file was a collection of some distant loci in a single chromosome, so maybe there were instances where the --indep-pairwise window fell over a VERY distantly located set of SNPs and found they were correlated, so they went into the 'prune.in' file. But then, during the --show-tags analysis there is a 240kb default 'window' where SNPs further apart than that are not examined for tagging. but I find it hard to swallow that I would get so many lines where a SNP is not tagging OR tagged just because some comparisons won't be made the second time around in --show-tags. 

What am I missing here? I've seen other peoples output from the same process posted with "None" in the TAGS column, but no one seems to bat an eye. I feel like I am overlooking something obvious here and I was hoping you could point it out to me. 

Many thanks in advance!


It's the .prune.out SNPs which are guaranteed to have r^2 > .7 with another SNP here.  A .prune.in SNPs might tag other SNPs, or it might just tag itself.