Package picard.analysis
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.
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Field Summary
FieldsModifier and TypeFieldDescriptionlong
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
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Constructor Summary
Constructors -
Method Summary
Methods inherited from class htsjdk.samtools.metrics.MetricBase
equals, hashCode, toString
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Field Details
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ACCUMULATION_LEVEL
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READS_USED
This option is used to mark including or excluding duplicates. -
WINDOW_SIZE
public int WINDOW_SIZEThe window size on the genome used to calculate the GC of the sequence. -
TOTAL_CLUSTERS
public long TOTAL_CLUSTERSThe total number of clusters that were seen in the gc bias calculation. -
ALIGNED_READS
public long ALIGNED_READSThe total number of aligned reads used to compute the gc bias metrics. -
AT_DROPOUT
public double AT_DROPOUTIllumina-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_DROPOUTIllumina-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_19Normalized coverage over quintile of GC content ranging from 0 - 19. -
GC_NC_20_39
public double GC_NC_20_39Normalized coverage over each quintile of GC content ranging from 20 - 39. -
GC_NC_40_59
public double GC_NC_40_59Normalized coverage over each quintile of GC content ranging from 40 - 59. -
GC_NC_60_79
public double GC_NC_60_79Normalized coverage over each quintile of GC content ranging from 60 - 79. -
GC_NC_80_100
public double GC_NC_80_100Normalized coverage over each quintile of GC content ranging from 80 - 100.
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Constructor Details
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GcBiasSummaryMetrics
public GcBiasSummaryMetrics()
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