I am new to the field of genomics and have only once or twice uses the bcftools before. I have to run a LMM using RVtests (it takes vcf format as input) for which I need to calculate a kinship matrix. In order to estimate the kinship matrix for each chromosome, I need to prune the vcf file for each chromosome based on a r2 0.25. Going through some earlier posts, I understood that I can use bcftools query. I would really appreciate if someone can suggest me a command line option for pruning a chromosome vcf file and obtaining a file with pruned in snps.