I have just started using bcftools to 'prune' some vcf files. While I have found some helpful examples of how to discard SNPs with high LD:
bcftools +prune -l 0.6 -w 1000 frag.vcf -Ov -o output1.vcf
I was hoping to actually create output where the SNPs kept were those with r2 values higher than .6, and the other SNPs are discarded. Is there a straightforward way to do this?