code: def _calculate_sv_coverage_gatk(data, work_dir):
      
      from bcbio.variation import coverage
      from bcbio.structural import annotate
      # GATK compatible
      target_file = gatkcnv.collect_read_counts(data, work_dir)
      # heterogeneity compatible
      target_in = bedutils.clean_file(tz.get_in(["regions", "bins", "target"], data), data, bedprep_dir=work_dir)
      target_cov = coverage.run_mosdepth(data, "target-gatk", target_in)
      target_cov_genes = annotate.add_genes(target_cov.regions, data, max_distance=0)
      return target_file, target_cov_genes
docs: Calculate coverage in defined regions using GATK tools
  
      TODO: This does double calculations to get GATK4 compatible HDF read counts
      and then depth and gene annotations. Both are needed for creating heterogeneity inputs.
      Ideally replace with a single mosdepth coverage calculation, and creat GATK4 TSV format:
  
      CONTIG  START   END     COUNT
      chrM    1       1000    13268