Package picard.analysis.directed
Class TargetMetrics
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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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- picard.analysis.directed.TargetMetrics
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public class TargetMetrics extends TargetMetricsBase
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 double
FOLD_ENRICHMENT
The fold by which the probed region has been amplified above genomic background, (ON_PROBE_BASES/(ON_PROBE_BASES + NEAR_PROBE_BASES + OFF_PROBE_BASES))/(PROBE_TERRITORY/GENOME_SIZE)double
MEAN_PROBE_COVERAGE
The mean coverage of all probes in the experiment, ON_PROBE_BASES/PROBE_TERRITORY.long
NEAR_PROBE_BASES
The number of PF aligned bases that mapped to within a fixed interval of a probed region, but not on a probed region.long
OFF_PROBE_BASES
The number of PF aligned bases that mapped to neither on or near a probe.long
ON_PROBE_BASES
The number of PF aligned probed bases that mapped to a baited region of the genome.double
ON_PROBE_VS_SELECTED
The fraction of on+near probe bases that are on as opposed to near, ON_PROBE_BASES/(ON_PROBE_BASES + NEAR_PROBE_BASES).double
PCT_OFF_PROBE
The fraction of aligned PF bases that mapped neither on or near a probe, OFF_PROBE_BASES/(ON_PROBE_BASES + NEAR_PROBE_BASES + OFF_PROBE_BASES).double
PCT_SELECTED_BASES
The fraction of bases that map on or near a probe (ON_PROBE_BASES + NEAR_PROBE_BASES)/(ON_PROBE_BASES + NEAR_PROBE_BASES + OFF_PROBE_BASES).String
PROBE_SET
The name of the PROBE_SET (BAIT_SET, AMPLICON_SET, ...) used in this metrics collection runlong
PROBE_TERRITORY
The number of unique bases covered by the intervals of all probes in the probe set-
Fields inherited from class picard.analysis.directed.TargetMetricsBase
ON_TARGET_FROM_PAIR_BASES, PF_SELECTED_PAIRS, PF_SELECTED_UNIQUE_PAIRS
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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 TargetMetrics()
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Field Detail
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PROBE_SET
public String PROBE_SET
The name of the PROBE_SET (BAIT_SET, AMPLICON_SET, ...) used in this metrics collection run
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PROBE_TERRITORY
public long PROBE_TERRITORY
The number of unique bases covered by the intervals of all probes in the probe set
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ON_PROBE_BASES
public long ON_PROBE_BASES
The number of PF aligned probed bases that mapped to a baited region of the genome.
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NEAR_PROBE_BASES
public long NEAR_PROBE_BASES
The number of PF aligned bases that mapped to within a fixed interval of a probed region, but not on a probed region.
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OFF_PROBE_BASES
public long OFF_PROBE_BASES
The number of PF aligned bases that mapped to neither on or near a probe.
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PCT_SELECTED_BASES
public double PCT_SELECTED_BASES
The fraction of bases that map on or near a probe (ON_PROBE_BASES + NEAR_PROBE_BASES)/(ON_PROBE_BASES + NEAR_PROBE_BASES + OFF_PROBE_BASES).
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PCT_OFF_PROBE
public double PCT_OFF_PROBE
The fraction of aligned PF bases that mapped neither on or near a probe, OFF_PROBE_BASES/(ON_PROBE_BASES + NEAR_PROBE_BASES + OFF_PROBE_BASES).
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ON_PROBE_VS_SELECTED
public double ON_PROBE_VS_SELECTED
The fraction of on+near probe bases that are on as opposed to near, ON_PROBE_BASES/(ON_PROBE_BASES + NEAR_PROBE_BASES).
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MEAN_PROBE_COVERAGE
public double MEAN_PROBE_COVERAGE
The mean coverage of all probes in the experiment, ON_PROBE_BASES/PROBE_TERRITORY.
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FOLD_ENRICHMENT
public double FOLD_ENRICHMENT
The fold by which the probed region has been amplified above genomic background, (ON_PROBE_BASES/(ON_PROBE_BASES + NEAR_PROBE_BASES + OFF_PROBE_BASES))/(PROBE_TERRITORY/GENOME_SIZE)
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