code: def annotate_with_depth(in_file, items):
      
      bam_file = None
      if len(items) == 1:
          bam_file = dd.get_align_bam(items[0])
      else:
          paired = vcfutils.get_paired(items)
          if paired:
              bam_file = paired.tumor_bam
      if bam_file:
          out_file = "%s-duphold.vcf.gz" % utils.splitext_plus(in_file)[0]
          if not utils.file_exists(out_file):
              with file_transaction(items[0], out_file) as tx_out_file:
                  if not in_file.endswith(".gz"):
                      in_file = vcfutils.bgzip_and_index(in_file, remove_orig=False,
                                                         out_dir=os.path.dirname(tx_out_file))
                  ref_file = dd.get_ref_file(items[0])
                  # cores for BAM reader thread, so max out at 4 based on recommendations
                  cores = min([dd.get_num_cores(items[0]), 4])
                  cmd = ("duphold --threads {cores} --vcf {in_file} --bam {bam_file} --fasta {ref_file} "
                         "-o {tx_out_file}")
                  do.run(cmd.format(**locals()), "Annotate SV depth with duphold")
          vcfutils.bgzip_and_index(out_file)
          return out_file
      else:
          return in_file
docs: Annotate called VCF file with depth using duphold (https://github.com/brentp/duphold)
  
      Currently annotates single sample and tumor samples in somatic analysis.