LD filter for GWAS with plink

Question

[biosol]

Hi all,

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 plink --excludecommand.

Thanks for the help in advance!

[zx8754]

Related posts:

• Filtering SNPS by minimum LD value in bcftools?
• Using vcftools to filter SNPs by a linkage disequilibrium (r2) threshold

[Kevin Blighe]

I have not seen any way to directly remove these with PLINK. I do not believe it is too much effort to have to use 2 commands, and it also helps with documentation by producing the output list of SNPs that are in / not in LD.