code: def sample_callable_bed(bam_file, ref_file, data):
      
      from bcbio.heterogeneity import chromhacks
      CovInfo = collections.namedtuple("CovInfo", "callable, raw_callable, depth_files")
      noalt_calling = "noalt_calling" in dd.get_tools_on(data) or "altcontigs" in dd.get_exclude_regions(data)
      def callable_chrom_filter(r):
          """Filter to callable region, potentially limiting by chromosomes.
          """
          return r.name == "CALLABLE" and (not noalt_calling or chromhacks.is_nonalt(r.chrom))
      out_file = "%s-callable_sample.bed" % os.path.splitext(bam_file)[0]
      with shared.bedtools_tmpdir(data):
          sv_bed = regions.get_sv_bed(data)
          callable_bed, depth_files = coverage.calculate(bam_file, data, sv_bed)
          input_regions_bed = dd.get_variant_regions(data)
          if not utils.file_uptodate(out_file, callable_bed):
              with file_transaction(data, out_file) as tx_out_file:
                  callable_regions = pybedtools.BedTool(callable_bed)
                  filter_regions = callable_regions.filter(callable_chrom_filter)
                  if input_regions_bed:
                      if not utils.file_uptodate(out_file, input_regions_bed):
                          input_regions = pybedtools.BedTool(input_regions_bed)
                          filter_regions.intersect(input_regions, nonamecheck=True).saveas(tx_out_file)
                  else:
                      filter_regions.saveas(tx_out_file)
      return CovInfo(out_file, callable_bed, depth_files)
docs: Retrieve callable regions for a sample subset by defined analysis regions.