I'm trying to remove SNPs that are in linkage disequilibrium (r2 = 0.8) from my GWAS dataset. For the moment, I've been trying the following command:
plink --vcf myvcf.vcf --const-fid 0 --r2 --ld-window-r2 0.8 --recode vcf --out myvcf.out
It actually works and generates a
.ldoutput file with pairwise r2 values for the SNPs. However, I was wondering if there is a method that directly removes those SNPs from the
.vcfinstead of having to pass the output list given in the
.ldfile to another
Thanks for the help in advance!