Class GcBiasSummaryMetrics


  • @DocumentedFeature(groupName="Metrics",
                       summary="Metrics")
    public class GcBiasSummaryMetrics
    extends MultilevelMetrics
    High level metrics that capture how biased the coverage in a certain lane is.
    • Field Summary

      Fields 
      Modifier and Type Field Description
      String ACCUMULATION_LEVEL  
      long ALIGNED_READS
      The total number of aligned reads used to compute the gc bias metrics.
      double AT_DROPOUT
      Illumina-style AT dropout metric.
      double GC_DROPOUT
      Illumina-style GC dropout metric.
      double GC_NC_0_19
      Normalized coverage over quintile of GC content ranging from 0 - 19.
      double GC_NC_20_39
      Normalized coverage over each quintile of GC content ranging from 20 - 39.
      double GC_NC_40_59
      Normalized coverage over each quintile of GC content ranging from 40 - 59.
      double GC_NC_60_79
      Normalized coverage over each quintile of GC content ranging from 60 - 79.
      double GC_NC_80_100
      Normalized coverage over each quintile of GC content ranging from 80 - 100.
      String READS_USED
      This option is used to mark including or excluding duplicates.
      long TOTAL_CLUSTERS
      The total number of clusters that were seen in the gc bias calculation.
      int WINDOW_SIZE
      The window size on the genome used to calculate the GC of the sequence.
    • Field Detail

      • ACCUMULATION_LEVEL

        public String ACCUMULATION_LEVEL
      • READS_USED

        public String READS_USED
        This option is used to mark including or excluding duplicates.
      • WINDOW_SIZE

        public int WINDOW_SIZE
        The window size on the genome used to calculate the GC of the sequence.
      • TOTAL_CLUSTERS

        public long TOTAL_CLUSTERS
        The total number of clusters that were seen in the gc bias calculation.
      • ALIGNED_READS

        public long ALIGNED_READS
        The total number of aligned reads used to compute the gc bias metrics.
      • AT_DROPOUT

        public double AT_DROPOUT
        Illumina-style AT dropout metric. Calculated by taking each GC bin independently and calculating (%ref_at_gc - %reads_at_gc) and summing all positive values for GC=[0..50].
      • GC_DROPOUT

        public double GC_DROPOUT
        Illumina-style GC dropout metric. Calculated by taking each GC bin independently and calculating (%ref_at_gc - %reads_at_gc) and summing all positive values for GC=[50..100].
      • GC_NC_0_19

        public double GC_NC_0_19
        Normalized coverage over quintile of GC content ranging from 0 - 19.
      • GC_NC_20_39

        public double GC_NC_20_39
        Normalized coverage over each quintile of GC content ranging from 20 - 39.
      • GC_NC_40_59

        public double GC_NC_40_59
        Normalized coverage over each quintile of GC content ranging from 40 - 59.
      • GC_NC_60_79

        public double GC_NC_60_79
        Normalized coverage over each quintile of GC content ranging from 60 - 79.
      • GC_NC_80_100

        public double GC_NC_80_100
        Normalized coverage over each quintile of GC content ranging from 80 - 100.
    • Constructor Detail

      • GcBiasSummaryMetrics

        public GcBiasSummaryMetrics()