picard.analysis

Class GcBiasSummaryMetrics

java.lang.Object

htsjdk.samtools.metrics.MetricBase

picard.analysis.GcBiasSummaryMetrics

public class GcBiasSummaryMetrics
extends htsjdk.samtools.metrics.MetricBase

High level metrics that capture how biased the coverage in a certain lane is.

Field Summary

Fields

Modifier and Type	Field and Description
int	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.
int	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.

Constructor Summary

Constructors

Constructor and Description
GcBiasSummaryMetrics()

Method Summary

Methods inherited from class htsjdk.samtools.metrics.MetricBase

equals, equals, hashCode, toString

Methods inherited from class java.lang.Object

clone, finalize, getClass, notify, notifyAll, wait, wait, wait

Field Detail

WINDOW_SIZE

public int WINDOW_SIZE

The window size on the genome used to calculate the GC of the sequence.

TOTAL_CLUSTERS

public int TOTAL_CLUSTERS

The total number of clusters that were seen in the gc bias calculation.

ALIGNED_READS

public int 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].

Constructor Detail

GcBiasSummaryMetrics

public GcBiasSummaryMetrics()