Class GcBiasDetailMetrics

java.lang.Object
htsjdk.samtools.metrics.MetricBase
picard.metrics.MultilevelMetrics
picard.analysis.GcBiasDetailMetrics

@DocumentedFeature(groupName="Metrics", summary="Metrics") public class GcBiasDetailMetrics extends MultilevelMetrics
Class that holds detailed metrics about reads that fall within windows of a certain GC bin on the reference genome.
  • Field Summary

    Fields
    Modifier and Type
    Field
    Description
     
    double
    The radius of error bars in this bin based on the number of observations made.
    int
    The G+C content of the reference sequence represented by this bin.
    int
    The mean quality (determined via the error rate) of all bases of all reads that are assigned to windows of this GC.
    double
    The ratio of "coverage" in this GC bin vs.
    long
    The number of reads whose start position is at the start of a window of this GC.
    This option is used to mark including or excluding duplicates.
    int
    The number of windows on the reference genome that have this G+C content.

    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.
    • GC

      public int GC
      The G+C content of the reference sequence represented by this bin. Values are from 0% to 100%
    • WINDOWS

      public int WINDOWS
      The number of windows on the reference genome that have this G+C content.
    • READ_STARTS

      public long READ_STARTS
      The number of reads whose start position is at the start of a window of this GC.
    • MEAN_BASE_QUALITY

      public int MEAN_BASE_QUALITY
      The mean quality (determined via the error rate) of all bases of all reads that are assigned to windows of this GC.
    • NORMALIZED_COVERAGE

      public double NORMALIZED_COVERAGE
      The ratio of "coverage" in this GC bin vs. the mean coverage of all GC bins. A number of 1 represents mean coverage, a number less than one represents lower than mean coverage (e.g. 0.5 means half as much coverage as average) while a number greater than one represents higher than mean coverage (e.g. 3.1 means this GC bin has 3.1 times more reads per window than average).
    • ERROR_BAR_WIDTH

      public double ERROR_BAR_WIDTH
      The radius of error bars in this bin based on the number of observations made. For example if the normalized coverage is 0.75 and the error bar width is 0.1 then the error bars would be drawn from 0.65 to 0.85.
  • Constructor Details

    • GcBiasDetailMetrics

      public GcBiasDetailMetrics()