picard.analysis

Class GcBiasSummaryMetrics

java.lang.Object

htsjdk.samtools.metrics.MetricBase

picard.metrics.MultilevelMetrics

picard.analysis.GcBiasSummaryMetrics

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 and Description
java.lang.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.
java.lang.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.

Fields inherited from class picard.metrics.MultilevelMetrics

LIBRARY, READ_GROUP, SAMPLE

Constructor Summary

Constructors

Constructor and Description
GcBiasSummaryMetrics()

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 Detail

ACCUMULATION_LEVEL

public java.lang.String ACCUMULATION_LEVEL

READS_USED

public java.lang.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()