Package picard.analysis.directed
Class TargetMetricsBase
- java.lang.Object
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- htsjdk.samtools.metrics.MetricBase
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- picard.metrics.MultilevelMetrics
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- picard.analysis.directed.PanelMetricsBase
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- picard.analysis.directed.TargetMetricsBase
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- Direct Known Subclasses:
TargetedPcrMetrics
,TargetMetrics
public class TargetMetricsBase extends PanelMetricsBase
TargetMetrics, are metrics to measure how well we hit specific targets (or baits) when using a targeted sequencing process like hybrid selection or Targeted PCR Techniques (TSCA). TargetMetrics at the moment are the metrics that are shared by both HybridSelection and TargetedPcrMetrics.
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Field Summary
Fields Modifier and Type Field Description long
ON_TARGET_FROM_PAIR_BASES
The number of PF aligned bases that are mapped in pair to a targeted region of the genome.long
PF_SELECTED_PAIRS
Tracks the number of read pairs that we see that are PF (used to calculate library size)long
PF_SELECTED_UNIQUE_PAIRS
Tracks the number of unique PF_SELECTED_PAIRS we see (used to calc library size)-
Fields inherited from class picard.analysis.directed.PanelMetricsBase
AT_DROPOUT, FOLD_80_BASE_PENALTY, GC_DROPOUT, GENOME_SIZE, HET_SNP_Q, HET_SNP_SENSITIVITY, MAX_TARGET_COVERAGE, MEAN_TARGET_COVERAGE, MEDIAN_TARGET_COVERAGE, MIN_TARGET_COVERAGE, ON_TARGET_BASES, PCT_EXC_ADAPTER, PCT_EXC_BASEQ, PCT_EXC_DUPE, PCT_EXC_MAPQ, PCT_EXC_OFF_TARGET, PCT_EXC_OVERLAP, PCT_PF_READS, PCT_PF_UQ_READS, PCT_PF_UQ_READS_ALIGNED, PCT_TARGET_BASES_100X, PCT_TARGET_BASES_10X, PCT_TARGET_BASES_1X, PCT_TARGET_BASES_20X, PCT_TARGET_BASES_2X, PCT_TARGET_BASES_30X, PCT_TARGET_BASES_40X, PCT_TARGET_BASES_50X, PF_BASES, PF_BASES_ALIGNED, PF_READS, PF_UNIQUE_READS, PF_UQ_BASES_ALIGNED, PF_UQ_READS_ALIGNED, TARGET_TERRITORY, TOTAL_READS, ZERO_CVG_TARGETS_PCT
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Fields inherited from class picard.metrics.MultilevelMetrics
LIBRARY, READ_GROUP, SAMPLE
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Constructor Summary
Constructors Constructor Description TargetMetricsBase()
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Field Detail
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PF_SELECTED_PAIRS
public long PF_SELECTED_PAIRS
Tracks the number of read pairs that we see that are PF (used to calculate library size)
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PF_SELECTED_UNIQUE_PAIRS
public long PF_SELECTED_UNIQUE_PAIRS
Tracks the number of unique PF_SELECTED_PAIRS we see (used to calc library size)
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ON_TARGET_FROM_PAIR_BASES
public long ON_TARGET_FROM_PAIR_BASES
The number of PF aligned bases that are mapped in pair to a targeted region of the genome.
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