minimum snp number from set in LD

Question

[RNAseqer]

ok I have run things through plink and I have a list of SNPs from a file. I want to know how much information these snps contain, for instance if one of those snps is in ld with another, that second one doesnt give you additional info. I need to find out just how much info my list of snps is giving me. Is there a way in plink or some other program to calculate the smallest number of snps that contains all of the information these linked snps convey?

Answer 1

[MatthewP]

Hello, If you need to remove LD snps, use --indep-pairwise of PLINK to get those snp list, then use --extract to remove LD snps. I think this step by step tutorial can help you learn QC in GWAS.

[RNAseqer]

Thank you. But my issue is actually this: here is my list of snps, they are all in this list of snps with r2>.7 relationships. How many actually informative snps do i have in my list? In other words if I have 27 snps, bu maybe between their linkage im only actually getting 7 pieces of uniq information. I was looking at haploviews tagger but im having trouble getting it to run, and am frankly unsure its the right program for the job. is their an easier way? Maybe a perl based program with a simpler interface? Im looking at a few thousand snps in each file that contains my snps of interest.