code: def _subset_to_variant_regions(callable_file, variant_regions, data):
      
      out_file = "%s-vrsubset.bed" % utils.splitext_plus(callable_file)[0]
      if not utils.file_uptodate(out_file, callable_file):
          with file_transaction(data, out_file) as tx_out_file:
              with utils.open_gzipsafe(callable_file) as in_handle:
                  pybedtools.BedTool(in_handle).intersect(variant_regions).saveas(tx_out_file)
      return out_file
docs: Subset output callable file to only variant regions of interest.