Question: Prune SNPs in LD with a list of SNPs
gravatar for aritra90
9 months ago by
United States
aritra9040 wrote:


I have a list of SNPs. I want to find the SNPs in a genotype (Plink format) data set, which are in LD (> 0.2) with the list of SNPs. Any help on how to achieve this is appreciated.


ld plink snp • 433 views
ADD COMMENTlink written 9 months ago by aritra9040

What have you tried? The plink online manuals are very extensive.

ADD REPLYlink modified 9 months ago • written 9 months ago by zx87547.7k

I couldn't figure out the right command to enter a SNP list and a genotype file and obtain another snp list which are in high LD. For now I've been using indep-pairwise to remove the SNPs in high LD beforehand and then do downstream analyses. However, I wanted to remove SNPs which are in LD with a particular subset of SNPs (provided in a file such as what --extract/--exclude takes in as input)

ADD REPLYlink written 9 months ago by aritra9040

Not sure but you may try the --ld-snp-list flag, which accepts a file-listing of input SNPs for the purpose of identifying LD.

ADD REPLYlink written 8 months ago by Kevin Blighe45k
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