How to get minimal Tagger SNPs by show-tags command?

[Kelvin]

Hi Christopher,

    I try me best to get a tagger SNPs list by --show-tags command. But I am confues by several questions. Could you explain for me?

1. I get a snplist by --write-snplist flag:

plink --bfile obes_range36_qc --maf 0.01 --geno 0.05 --write-snplist --out obes_range36_qc.snplist

then I use --show-tags flag:

plink --bfile obes_range36_qc --show-tags obes_range36_qc.snplist --tag-r2 0.8 --tag-kb 250  --out obes_range36_tags

Qustion 1:the output file just list all 670 snps in the snplist, but I don't know which is tagger snp?

Then I add  --list-all, and I  filter snp by NTAG>2, I got a 98 snp list, output file is obes_range36_tags5_ntags_morethan2_list_98.txt

plink --bfile obes_range36_qc --show-tags obes_range36_tags5_ntags_morethan2_list_98.txt --tag-r2 0.8 --tag-kb 250  --out obes_range36_tags.tags

This time added 11 snps,the total is 109 snps.

Question 2: this 109 snps list is the tagger snp list?

I can add the --tag-mode2 command to specify an alternative input and output format. In this case, we assume the input file contains two columns, with the second field being either 0 or 1 to indicate whether or not this is a target SNP:

Question 3: Before I run show-tags, I don't know which snp is taget SNP, how do I prepare the input file? I most concern that how can I  pick the minimal set of SNPs required to tag all common variation in a region?

I study PLINK 1.9 help function about --show-tags, new version add --ld-xchr code(1/2/3), can I control r2 to get indepedent SNP with r2<0.2? It is very usful and important,but  I can just select code 1,2 or 3 now.

In sammary, How can I get a minimal Tagger SNP set by PLINK command?

By the way, I think PLINK1.07 function description is very clear and there are plenty example(http://pngu.mgh.harvard.edu/~purcell/plink/). I surgest you keep this style. But I often lost in PLINK 1.9 function description(https://www.cog-genomics.org/plink2/).

Best to you.

Kelvin Liu

[Christopher Chang]

To get a minimal set of tagging SNPs, use --indep-pairwise or --indep-pairphase.  *After* you have that SNP list (the .prune.in file), you can use --show-tags + --list-all to see which of those SNPs are tagging which other SNPs.

--ld-xchr only affects the X chromosome; it does not sound relevant to your immediate problem.

Yes, the current 1.9 documentation is more of a supplement for people migrating from 1.07 than an entirely self-contained manual, and this should be changed at some point; thanks for reporting your confusion.