Class GcBiasSummaryMetrics

java.lang.Object
htsjdk.samtools.metrics.MetricBase
picard.metrics.MultilevelMetrics
picard.analysis.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
     
    long
    The total number of aligned reads used to compute the gc bias metrics.
    double
    Illumina-style AT dropout metric.
    double
    Illumina-style GC dropout metric.
    double
    Normalized coverage over quintile of GC content ranging from 0 - 19.
    double
    Normalized coverage over each quintile of GC content ranging from 20 - 39.
    double
    Normalized coverage over each quintile of GC content ranging from 40 - 59.
    double
    Normalized coverage over each quintile of GC content ranging from 60 - 79.
    double
    Normalized coverage over each quintile of GC content ranging from 80 - 100.
    This option is used to mark including or excluding duplicates.
    long
    The total number of clusters that were seen in the gc bias calculation.
    int
    The window size on the genome used to calculate the GC of the sequence.

    Fields inherited from class picard.metrics.MultilevelMetrics

    LIBRARY, READ_GROUP, SAMPLE
  • Constructor Summary

    Constructors
    Constructor
    Description
     
  • Method Summary

    Methods inherited from class htsjdk.samtools.metrics.MetricBase

    equals, hashCode, toString

    Methods inherited from class java.lang.Object

    clone, finalize, getClass, notify, notifyAll, wait, wait, wait
  • Field Details

    • 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 Details

    • GcBiasSummaryMetrics

      public GcBiasSummaryMetrics()