code: def _prep_subsampled_bams(data, work_dir):
      
      sr_bam, disc_bam = sshared.get_split_discordants(data, work_dir)
      ds_bam = bam.downsample(dd.get_align_bam(data), data, 1e8,
                              read_filter="-F 'not secondary_alignment and proper_pair'",
                              always_run=True, work_dir=work_dir)
      out_bam = "%s-final%s" % utils.splitext_plus(ds_bam)
      if not utils.file_exists(out_bam):
          bam.merge([ds_bam, sr_bam, disc_bam], out_bam, data["config"])
      bam.index(out_bam, data["config"])
      return [out_bam]
docs: Prepare a subsampled BAM file with discordants from samblaster and minimal correct pairs.
  
      This attempts to minimize run times by pre-extracting useful reads mixed
      with subsampled normal pairs to estimate paired end distributions:
  
      https://groups.google.com/d/msg/delly-users/xmia4lwOd1Q/uaajoBkahAIJ
  
      Subsamples correctly aligned reads to 100 million based on speedseq defaults and
      evaluations on NA12878 whole genome data:
  
      https://github.com/cc2qe/speedseq/blob/ca624ba9affb0bd0fb88834ca896e9122639ec94/bin/speedseq#L1102
  
      XXX Currently not used as new versions of delly do not get good sensitivity
      with downsampled BAMs.