Class CollectQualityYieldMetricsSNVQ.QualityYieldMetrics

java.lang.Object
htsjdk.samtools.metrics.MetricBase
picard.analysis.MergeableMetricBase
picard.analysis.CollectQualityYieldMetricsSNVQ.QualityYieldMetrics
Enclosing class:
CollectQualityYieldMetricsSNVQ
@DocumentedFeature(groupName="Metrics", summary="Metrics") public static class CollectQualityYieldMetricsSNVQ.QualityYieldMetrics extends MergeableMetricBase
A set of metrics used to describe the general quality of a BAM file

  • Field Details

    • TOTAL_READS

      public long TOTAL_READS
      The total number of reads in the input file

    • PF_READS

      public long PF_READS
      The number of reads that are PF - pass filter

    • READ_LENGTH

      public int READ_LENGTH
      The average read length of all the reads

    • TOTAL_BASES

      public long TOTAL_BASES
      The total number of bases in all reads

    • PF_BASES

      public long PF_BASES
      The total number of bases in all PF reads

    • Q20_BASES

      public long Q20_BASES
      The number of bases in all reads that achieve quality score 20 or higher

    • PF_Q20_BASES

      public long PF_Q20_BASES
      The number of bases in PF reads that achieve quality score 20 or higher

    • Q30_BASES

      public long Q30_BASES
      The number of bases in all reads that achieve quality score 30 or higher

    • PF_Q30_BASES

      public long PF_Q30_BASES
      The number of bases in PF reads that achieve quality score 30 or higher

    • Q40_BASES

      public long Q40_BASES
      The number of bases in all reads that achieve quality score 40 or higher

    • PF_Q40_BASES

      public long PF_Q40_BASES
      The number of bases in PF reads that achieve quality score 40 or higher

    • PCT_Q20_BASES

      public double PCT_Q20_BASES
      The percentage of SNVQ values in all reads that achieve quality score 20 or higher

    • PCT_Q30_BASES

      public double PCT_Q30_BASES
      The percentage of SNVQ values in all reads that achieve quality score 30 or higher

    • PCT_Q40_BASES

      public double PCT_Q40_BASES
      The percentage of SNVQ values in all reads that achieve quality score 40 or higher

    • PCT_PF_Q20_BASES

      public double PCT_PF_Q20_BASES
      The percentage of SNVQ values in all reads that achieve quality score 20 or higher and pass filter

    • PCT_PF_Q30_BASES

      public double PCT_PF_Q30_BASES
      The percentage of SNVQ values in all reads that achieve quality score 30 or higher and pass filter

    • PCT_PF_Q40_BASES

      public double PCT_PF_Q40_BASES
      The percentage of SNVQ values in all reads that achieve quality score 40 or higher and pass filter

    • TOTAL_SNVQ

      public long TOTAL_SNVQ
      The total number of SNVQ values in all reads

    • PF_SNVQ

      public long PF_SNVQ
      The total number of SNVQ values in all PF reads

    • Q20_SNVQ

      public long Q20_SNVQ
      The number of SNVQ values in all reads that achieve quality score 20 or higher

    • PF_Q20_SNVQ

      public long PF_Q20_SNVQ
      The number of SNVQ values in PF reads that achieve quality score 20 or higher

    • Q30_SNVQ

      public long Q30_SNVQ
      The number of SNVQ values in all reads that achieve quality score 30 or higher

    • PF_Q30_SNVQ

      public long PF_Q30_SNVQ
      The number of SNVQ values in PF reads that achieve quality score 30 or higher

    • Q40_SNVQ

      public long Q40_SNVQ
      The number of SNVQ values in all reads that achieve quality score 40 or higher

    • PF_Q40_SNVQ

      public long PF_Q40_SNVQ
      The number of SNVQ values in PF reads that achieve quality score 40 or higher

    • PCT_Q20_SNVQ

      public double PCT_Q20_SNVQ
      The percentage of SNVQ values in all reads that achieve quality score 20 or higher

    • PCT_Q30_SNVQ

      public double PCT_Q30_SNVQ
      The percentage of SNVQ values in all reads that achieve quality score 30 or higher

    • PCT_Q40_SNVQ

      public double PCT_Q40_SNVQ
      The percentage of SNVQ values in all reads that achieve quality score 40 or higher

    • PCT_PF_Q20_SNVQ

      public double PCT_PF_Q20_SNVQ
      The percentage of SNVQ values in all reads that achieve quality score 20 or higher and pass filter

    • PCT_PF_Q30_SNVQ

      public double PCT_PF_Q30_SNVQ
      The percentage of SNVQ values in all reads that achieve quality score 30 or higher and pass filter

    • PCT_PF_Q40_SNVQ

      public double PCT_PF_Q40_SNVQ
      The percentage of SNVQ values in all reads that achieve quality score 40 or higher and pass filter

    • alternateQualityAttribute

      protected final String alternateQualityAttribute

  • Constructor Details

    • QualityYieldMetrics

      public QualityYieldMetrics()

    • QualityYieldMetrics

      public QualityYieldMetrics(String alternateQualityAttribute)

  • Method Details