Package picard.analysis.directed
Class TargetedPcrMetrics
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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.TargetedPcrMetrics
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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
Fields Modifier and Type Field Description long
AMPLICON_TERRITORY
The number of unique bases covered by the intervals of all amplicons in the amplicon setString
CUSTOM_AMPLICON_SET
The name of the amplicon set used in this metrics collection rundouble
FOLD_ENRICHMENT
The fold by which the amplicon region has been amplified above genomic background.double
MEAN_AMPLICON_COVERAGE
The mean read coverage of all amplicon regions in the experiment.long
NEAR_AMPLICON_BASES
The number of PF_BASES_ALIGNED that mapped to within a fixed interval of an amplified region, but not on a baited region.long
OFF_AMPLICON_BASES
The number of PF_BASES_ALIGNED that mapped neither on or near an amplicon.long
ON_AMPLICON_BASES
The number of PF_BASES_ALIGNED that mapped to an amplified region of the genome.double
ON_AMPLICON_VS_SELECTED
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
PCT_AMPLIFIED_BASES
The fraction of PF_BASES_ALIGNED that mapped to or near an amplicon, (ON_AMPLICON_BASES + NEAR_AMPLICON_BASES)/PF_BASES_ALIGNED.double
PCT_OFF_AMPLICON
The fraction of PF_BASES_ALIGNED that mapped neither onto or near an amplicon, OFF_AMPLICON_BASES/PF_BASES_ALIGNED-
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_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
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Fields inherited from class picard.metrics.MultilevelMetrics
LIBRARY, READ_GROUP, SAMPLE
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Constructor Summary
Constructors Constructor Description TargetedPcrMetrics()
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Field Detail
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CUSTOM_AMPLICON_SET
public String CUSTOM_AMPLICON_SET
The name of the amplicon set used in this metrics collection run
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AMPLICON_TERRITORY
public long AMPLICON_TERRITORY
The number of unique bases covered by the intervals of all amplicons in the amplicon set
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ON_AMPLICON_BASES
public long ON_AMPLICON_BASES
The number of PF_BASES_ALIGNED that mapped to an amplified region of the genome.
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NEAR_AMPLICON_BASES
public long NEAR_AMPLICON_BASES
The number of PF_BASES_ALIGNED that mapped to within a fixed interval of an amplified region, but not on a baited region.
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OFF_AMPLICON_BASES
public long OFF_AMPLICON_BASES
The number of PF_BASES_ALIGNED that mapped neither on or near an amplicon.
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PCT_AMPLIFIED_BASES
public double PCT_AMPLIFIED_BASES
The fraction of PF_BASES_ALIGNED that mapped to or near an amplicon, (ON_AMPLICON_BASES + NEAR_AMPLICON_BASES)/PF_BASES_ALIGNED.
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PCT_OFF_AMPLICON
public double PCT_OFF_AMPLICON
The fraction of PF_BASES_ALIGNED that mapped neither onto or near an amplicon, OFF_AMPLICON_BASES/PF_BASES_ALIGNED
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ON_AMPLICON_VS_SELECTED
public double ON_AMPLICON_VS_SELECTED
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)
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MEAN_AMPLICON_COVERAGE
public double MEAN_AMPLICON_COVERAGE
The mean read coverage of all amplicon regions in the experiment.
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FOLD_ENRICHMENT
public double FOLD_ENRICHMENT
The fold by which the amplicon region has been amplified above genomic background.
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