code: def recalibrate_quality(bam_file, sam_ref, dbsnp_file, picard_dir):
      
      cl = ["picard_gatk_recalibrate.py", picard_dir, sam_ref, bam_file]
      if dbsnp_file:
          cl.append(dbsnp_file)
      subprocess.check_call(cl)
      out_file = glob.glob("%s*gatkrecal.bam" % os.path.splitext(bam_file)[0])[0]
      return out_file
docs: Recalibrate alignments with GATK and provide pdf summary.