code: def _pick_best_quality_score(vrn_file):
      
      # pysam fails on checking reference contigs if input is empty
      if not vcfutils.vcf_has_variants(vrn_file):
          return "DP"
      to_check = 25
      scores = collections.defaultdict(int)
      try:
          in_handle = VariantFile(vrn_file)
      except ValueError:
          raise ValueError("Failed to parse input file in preparation for validation: %s" % vrn_file)
      with contextlib.closing(in_handle) as val_in:
          for i, rec in enumerate(val_in):
              if i > to_check:
                  break
              if "VQSLOD" in rec.info and rec.info.get("VQSLOD") is not None:
                  scores["INFO=VQSLOD"] += 1
              if "TLOD" in rec.info and rec.info.get("TLOD") is not None:
                  scores["INFO=TLOD"] += 1
              for skey in ["AVR", "GQ", "DP"]:
                  if len(rec.samples) > 0 and rec.samples[0].get(skey) is not None:
                      scores[skey] += 1
              if rec.qual:
                  scores["QUAL"] += 1
      for key in ["AVR", "INFO=VQSLOD", "INFO=TLOD", "GQ", "QUAL", "DP"]:
          if scores[key] > 0:
              return key
      raise ValueError("Did not find quality score for validation from %s" % vrn_file)
docs: Flexible quality score selection, picking the best available.
  
      Implementation based on discussion:
  
      https://github.com/bcbio/bcbio-nextgen/commit/a538cecd86c0000d17d3f9d4f8ac9d2da04f9884#commitcomment-14539249
  
      (RTG=AVR/GATK=VQSLOD/MuTect=t_lod_fstar, otherwise GQ, otherwise QUAL, otherwise DP.)
  
      For MuTect, it's not clear how to get t_lod_fstar, the right quality score, into VCF cleanly.
      MuTect2 has TLOD in the INFO field.