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minimum snp number from set in LD

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?

snps ld minimum snp number
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updated by MatthewP MatthewP • written by RNAseqer RNAseqer

1 answer

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.

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written by MatthewP MatthewP

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.

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written by RNAseqer RNAseqer

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