Find overlap between VCF files I have two VCF files and I want to compare the missing rate in each of them, but I want to only look at sites that are present in both files.  How could I go about getting a list of positions that are included in both VCF files and then filtering those VCF files to only include those positions?
Something like vcf-isec? Quoting:


  Creates intersections and complements of two or more VCF files. Given multiple VCF files, it can output the list of positions which are shared by at least N files, at most N files, exactly N files, etc. The first example below outputs positions shared by at least two files and the second outputs positions present in the files A but absent from files B and C.