I'm using 1000 genomes vcfs, and I'm trying to thin out SNPs in moderate linkage disequlibrium (r2) using vcftools. In plink, I would do this using the --indep-pairwise parameter, and then excluding the outputted SNPs:
plink --bfile DATA --indep-pairwise 50 10 0.8 --out OUTPUT --noweb
plink --bfile DATA --exclude OUTPUT.prune.out --noweb --make-bed --out DATA_FILTERED
Does anyone know if there is an equivalent one or two step solution to do this using vcftools? I would like to avoid having to convert to plink format and back to vcf, if possible.
Thanks!