Yes, vcftools would be a great option. Check out for the manual:

http://vcftools.sourceforge.net/man_latest.html

You should be using something like:

vcftools --vcf input_file.vcf --exclude-positions --recode

*check out that the loci locations coincide in your VCF matrix and Bayescan file. Some outlier finding tools tend to sum+1 to the database, so that a locus (the same locus) that is 1234_567 in one file may be named 1234_568 in other one.