Package picard.analysis.directed
Class TargetedPcrMetrics
java.lang.Object
htsjdk.samtools.metrics.MetricBase
picard.metrics.MultilevelMetrics
picard.analysis.directed.PanelMetricsBase
picard.analysis.directed.TargetMetricsBase
picard.analysis.directed.TargetedPcrMetrics
@DocumentedFeature(groupName="Metrics",
summary="Metrics")
public class TargetedPcrMetrics
extends TargetMetricsBase
Metrics class for the analysis of reads obtained from targeted pcr experiments e.g. the TruSeq Custom Amplicon
(TSCA) kit (Illumina).
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Field Summary
FieldsModifier and TypeFieldDescriptionlong
The number of unique bases covered by the intervals of all amplicons in the amplicon setThe name of the amplicon set used in this metrics collection rundouble
The fold by which the amplicon region has been amplified above genomic background.double
The mean read coverage of all amplicon regions in the experiment.long
The number of PF_BASES_ALIGNED that mapped to within a fixed interval of an amplified region, but not on a baited region.long
The number of PF_BASES_ALIGNED that mapped neither on or near an amplicon.long
The number of PF_BASES_ALIGNED that mapped to an amplified region of the genome.double
The fraction of bases mapping to regions on or near amplicons, which mapped directly to but not near amplicons, ON_AMPLICON_BASES/(NEAR_AMPLICON_BASES + ON_AMPLICON_BASES)double
The fraction of PF_BASES_ALIGNED that mapped to or near an amplicon, (ON_AMPLICON_BASES + NEAR_AMPLICON_BASES)/PF_BASES_ALIGNED.double
The fraction of PF_BASES_ALIGNED that mapped neither onto or near an amplicon, OFF_AMPLICON_BASES/PF_BASES_ALIGNEDFields inherited from class picard.analysis.directed.TargetMetricsBase
ON_TARGET_FROM_PAIR_BASES, PF_SELECTED_PAIRS, PF_SELECTED_UNIQUE_PAIRS
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_100000X, PCT_TARGET_BASES_10000X, PCT_TARGET_BASES_1000X, PCT_TARGET_BASES_100X, PCT_TARGET_BASES_10X, PCT_TARGET_BASES_1X, PCT_TARGET_BASES_20X, PCT_TARGET_BASES_25000X, PCT_TARGET_BASES_2500X, PCT_TARGET_BASES_250X, PCT_TARGET_BASES_2X, PCT_TARGET_BASES_30X, PCT_TARGET_BASES_40X, PCT_TARGET_BASES_50000X, PCT_TARGET_BASES_5000X, PCT_TARGET_BASES_500X, 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
Fields inherited from class picard.metrics.MultilevelMetrics
LIBRARY, READ_GROUP, SAMPLE
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Constructor Summary
Constructors -
Method Summary
Methods inherited from class htsjdk.samtools.metrics.MetricBase
equals, hashCode, toString
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Field Details
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CUSTOM_AMPLICON_SET
The name of the amplicon set used in this metrics collection run -
AMPLICON_TERRITORY
public long AMPLICON_TERRITORYThe number of unique bases covered by the intervals of all amplicons in the amplicon set -
ON_AMPLICON_BASES
public long ON_AMPLICON_BASESThe number of PF_BASES_ALIGNED that mapped to an amplified region of the genome. -
NEAR_AMPLICON_BASES
public long NEAR_AMPLICON_BASESThe number of PF_BASES_ALIGNED that mapped to within a fixed interval of an amplified region, but not on a baited region. -
OFF_AMPLICON_BASES
public long OFF_AMPLICON_BASESThe number of PF_BASES_ALIGNED that mapped neither on or near an amplicon. -
PCT_AMPLIFIED_BASES
public double PCT_AMPLIFIED_BASESThe fraction of PF_BASES_ALIGNED that mapped to or near an amplicon, (ON_AMPLICON_BASES + NEAR_AMPLICON_BASES)/PF_BASES_ALIGNED. -
PCT_OFF_AMPLICON
public double PCT_OFF_AMPLICONThe fraction of PF_BASES_ALIGNED that mapped neither onto or near an amplicon, OFF_AMPLICON_BASES/PF_BASES_ALIGNED -
ON_AMPLICON_VS_SELECTED
public double ON_AMPLICON_VS_SELECTEDThe fraction of bases mapping to regions on or near amplicons, which mapped directly to but not near amplicons, ON_AMPLICON_BASES/(NEAR_AMPLICON_BASES + ON_AMPLICON_BASES) -
MEAN_AMPLICON_COVERAGE
public double MEAN_AMPLICON_COVERAGEThe mean read coverage of all amplicon regions in the experiment. -
FOLD_ENRICHMENT
public double FOLD_ENRICHMENTThe fold by which the amplicon region has been amplified above genomic background.
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Constructor Details
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TargetedPcrMetrics
public TargetedPcrMetrics()
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