I'm at a point where I would want to compute between population Weir and Cockerham Fst values directly from a large vcf file. Apparently VCFtools had utilities for this as in this question http://seqanswers.com/forums/showthread.php?t=34511 and the command were if I am correct:

vcftools --vcf input_file.vcf --weir-fst-pop Population1.txt --weir-fst-pop Population2.txt > Weir_Cockerham_fst.txt

How would I compute the same thing with BCFtools?

Thanks.