code: def _get_vqsr_annotations(filter_type, data):
      
      if filter_type == "SNP":
          # MQ, MQRankSum
          anns = ["QD", "FS", "ReadPosRankSum", "SOR"]
      else:
          assert filter_type == "INDEL"
          # MQRankSum
          anns = ["QD", "FS", "ReadPosRankSum", "SOR"]
      if dd.get_coverage_interval(data) == "genome":
          anns += ["DP"]
      return anns
docs: Retrieve appropriate annotations to use for VQSR based on filter type.
  
      Issues reported with MQ and bwa-mem quality distribution, results in intermittent
      failures to use VQSR:
      http://gatkforums.broadinstitute.org/discussion/4425/variant-recalibration-failing
      http://gatkforums.broadinstitute.org/discussion/4248/variantrecalibrator-removing-all-snps-from-the-training-set