Package picard.analysis
Class GcBiasSummaryMetrics
- java.lang.Object
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- htsjdk.samtools.metrics.MetricBase
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- picard.metrics.MultilevelMetrics
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- picard.analysis.GcBiasSummaryMetrics
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@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
Fields Modifier and Type Field Description 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.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
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Constructor Summary
Constructors Constructor Description GcBiasSummaryMetrics()
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Field Detail
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ACCUMULATION_LEVEL
public String ACCUMULATION_LEVEL
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READS_USED
public String READS_USED
This option is used to mark including or excluding duplicates.
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WINDOW_SIZE
public int WINDOW_SIZE
The window size on the genome used to calculate the GC of the sequence.
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TOTAL_CLUSTERS
public long TOTAL_CLUSTERS
The total number of clusters that were seen in the gc bias calculation.
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ALIGNED_READS
public long ALIGNED_READS
The total number of aligned reads used to compute the gc bias metrics.
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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].
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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].
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GC_NC_0_19
public double GC_NC_0_19
Normalized coverage over quintile of GC content ranging from 0 - 19.
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GC_NC_20_39
public double GC_NC_20_39
Normalized coverage over each quintile of GC content ranging from 20 - 39.
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GC_NC_40_59
public double GC_NC_40_59
Normalized coverage over each quintile of GC content ranging from 40 - 59.
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GC_NC_60_79
public double GC_NC_60_79
Normalized coverage over each quintile of GC content ranging from 60 - 79.
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GC_NC_80_100
public double GC_NC_80_100
Normalized coverage over each quintile of GC content ranging from 80 - 100.
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