Package picard.analysis.directed
Class PanelMetricsBase
java.lang.Object
htsjdk.samtools.metrics.MetricBase
picard.metrics.MultilevelMetrics
picard.analysis.directed.PanelMetricsBase
- Direct Known Subclasses:
HsMetrics
,TargetMetricsBase
A base class for Metrics for targeted panels. Metrics for library construction protocols based on
PCR amplicons/probes and Hybrid Selection baits are derived from this class.
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Field Summary
FieldsModifier and TypeFieldDescriptiondouble
A measure of how undercovered <= 50% GC regions are relative to the mean.double
The fold over-coverage necessary to raise 80% of bases in "non-zero-cvg" targets to the mean coverage level in those targets.double
A measure of how undercovered >= 50% GC regions are relative to the mean.long
The number of bases in the reference genome used for alignment.double
The Phred Scaled Q Score of the theoretical HET SNP sensitivity.double
The theoretical HET SNP sensitivity.long
The maximum coverage of reads that mapped to target regions of an experiment.double
The mean coverage of targets.double
The median coverage of targets.long
The minimum coverage of reads that mapped to target regions of an experiment.long
The number of PF aligned bases that mapped to a targeted region of the genome.double
The fraction of aligned bases in reads that have MQ=0 and whose 5' end consists of adapter sequence.double
The fraction of aligned bases that were filtered out because they were of low base quality.double
The fraction of aligned bases that were filtered out because they were in reads marked as duplicates.double
The fraction of aligned bases that were filtered out because they were in reads with low mapping quality.double
The fraction of aligned bases that were filtered out because they did not align over a target base.double
The fraction of aligned bases that were filtered out because they were the second observation from an insert with overlapping reads.double
The fraction of reads passing filter, PF_READS/TOTAL_READS.double
The fraction of unique reads passing filter, PF_UNIQUE_READS/TOTAL_READS.double
The fraction of unique reads passing filter that align to the reference, PF_UQ_READS_ALIGNED/PF_UNIQUE_READS.double
The fraction of all target bases achieving 100000X or greater coverage.double
The fraction of all target bases achieving 10000X or greater coverage.double
The fraction of all target bases achieving 1000X or greater coverage.double
The fraction of all target bases achieving 100X or greater coverage.double
The fraction of all target bases achieving 10X or greater coverage.double
The fraction of all target bases achieving 1X or greater coverage.double
The fraction of all target bases achieving 20X or greater coverage.double
The fraction of all target bases achieving 25000X or greater coverage.double
The fraction of all target bases achieving 2500X or greater coverage.double
The fraction of all target bases achieving 250X or greater coverage.double
The fraction of all target bases achieving 2X or greater coverage.double
The fraction of all target bases achieving 30X or greater coverage.double
The fraction of all target bases achieving 40X or greater coverage.double
The fraction of all target bases achieving 50000X or greater coverage.double
The fraction of all target bases achieving 5000X or greater coverage.double
The fraction of all target bases achieving 500X or greater coverage.double
The fraction of all target bases achieving 50X or greater coverage.long
The number of bases in the PF_READS of a SAM or BAM filelong
The number of PF_BASES that are aligned with mapping score > 0 to the reference genome.long
The number of passing filter reads (PF).long
The number of PF_READS that are not marked as duplicates.long
The number of PF unique bases that are aligned with mapping score > 0 to the reference genome.long
The number of PF_UNIQUE_READS that are aligned with mapping score > 0 to the reference genome.long
The number of unique bases covered by the intervals of all targets that should be coveredlong
The total number of reads in the SAM or BAM file examined.double
The fraction of targets that did not reach coverage=1 over any base.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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TARGET_TERRITORY
public long TARGET_TERRITORYThe number of unique bases covered by the intervals of all targets that should be covered -
GENOME_SIZE
public long GENOME_SIZEThe number of bases in the reference genome used for alignment. -
TOTAL_READS
public long TOTAL_READSThe total number of reads in the SAM or BAM file examined. -
PF_READS
public long PF_READSThe number of passing filter reads (PF). -
PF_BASES
public long PF_BASESThe number of bases in the PF_READS of a SAM or BAM file -
PF_UNIQUE_READS
public long PF_UNIQUE_READSThe number of PF_READS that are not marked as duplicates. -
PF_UQ_READS_ALIGNED
public long PF_UQ_READS_ALIGNEDThe number of PF_UNIQUE_READS that are aligned with mapping score > 0 to the reference genome. -
PF_BASES_ALIGNED
public long PF_BASES_ALIGNEDThe number of PF_BASES that are aligned with mapping score > 0 to the reference genome. -
PF_UQ_BASES_ALIGNED
public long PF_UQ_BASES_ALIGNEDThe number of PF unique bases that are aligned with mapping score > 0 to the reference genome. -
ON_TARGET_BASES
public long ON_TARGET_BASESThe number of PF aligned bases that mapped to a targeted region of the genome. -
PCT_PF_READS
public double PCT_PF_READSThe fraction of reads passing filter, PF_READS/TOTAL_READS. -
PCT_PF_UQ_READS
public double PCT_PF_UQ_READSThe fraction of unique reads passing filter, PF_UNIQUE_READS/TOTAL_READS. -
PCT_PF_UQ_READS_ALIGNED
public double PCT_PF_UQ_READS_ALIGNEDThe fraction of unique reads passing filter that align to the reference, PF_UQ_READS_ALIGNED/PF_UNIQUE_READS. -
MEAN_TARGET_COVERAGE
public double MEAN_TARGET_COVERAGEThe mean coverage of targets. -
MEDIAN_TARGET_COVERAGE
public double MEDIAN_TARGET_COVERAGEThe median coverage of targets. -
MAX_TARGET_COVERAGE
public long MAX_TARGET_COVERAGEThe maximum coverage of reads that mapped to target regions of an experiment. -
MIN_TARGET_COVERAGE
public long MIN_TARGET_COVERAGEThe minimum coverage of reads that mapped to target regions of an experiment. -
ZERO_CVG_TARGETS_PCT
public double ZERO_CVG_TARGETS_PCTThe fraction of targets that did not reach coverage=1 over any base. -
PCT_EXC_DUPE
public double PCT_EXC_DUPEThe fraction of aligned bases that were filtered out because they were in reads marked as duplicates. -
PCT_EXC_ADAPTER
public double PCT_EXC_ADAPTERThe fraction of aligned bases in reads that have MQ=0 and whose 5' end consists of adapter sequence. -
PCT_EXC_MAPQ
public double PCT_EXC_MAPQThe fraction of aligned bases that were filtered out because they were in reads with low mapping quality. -
PCT_EXC_BASEQ
public double PCT_EXC_BASEQThe fraction of aligned bases that were filtered out because they were of low base quality. -
PCT_EXC_OVERLAP
public double PCT_EXC_OVERLAPThe fraction of aligned bases that were filtered out because they were the second observation from an insert with overlapping reads. -
PCT_EXC_OFF_TARGET
public double PCT_EXC_OFF_TARGETThe fraction of aligned bases that were filtered out because they did not align over a target base. -
FOLD_80_BASE_PENALTY
public double FOLD_80_BASE_PENALTYThe fold over-coverage necessary to raise 80% of bases in "non-zero-cvg" targets to the mean coverage level in those targets. -
PCT_TARGET_BASES_1X
public double PCT_TARGET_BASES_1XThe fraction of all target bases achieving 1X or greater coverage. -
PCT_TARGET_BASES_2X
public double PCT_TARGET_BASES_2XThe fraction of all target bases achieving 2X or greater coverage. -
PCT_TARGET_BASES_10X
public double PCT_TARGET_BASES_10XThe fraction of all target bases achieving 10X or greater coverage. -
PCT_TARGET_BASES_20X
public double PCT_TARGET_BASES_20XThe fraction of all target bases achieving 20X or greater coverage. -
PCT_TARGET_BASES_30X
public double PCT_TARGET_BASES_30XThe fraction of all target bases achieving 30X or greater coverage. -
PCT_TARGET_BASES_40X
public double PCT_TARGET_BASES_40XThe fraction of all target bases achieving 40X or greater coverage. -
PCT_TARGET_BASES_50X
public double PCT_TARGET_BASES_50XThe fraction of all target bases achieving 50X or greater coverage. -
PCT_TARGET_BASES_100X
public double PCT_TARGET_BASES_100XThe fraction of all target bases achieving 100X or greater coverage. -
PCT_TARGET_BASES_250X
public double PCT_TARGET_BASES_250XThe fraction of all target bases achieving 250X or greater coverage. -
PCT_TARGET_BASES_500X
public double PCT_TARGET_BASES_500XThe fraction of all target bases achieving 500X or greater coverage. -
PCT_TARGET_BASES_1000X
public double PCT_TARGET_BASES_1000XThe fraction of all target bases achieving 1000X or greater coverage. -
PCT_TARGET_BASES_2500X
public double PCT_TARGET_BASES_2500XThe fraction of all target bases achieving 2500X or greater coverage. -
PCT_TARGET_BASES_5000X
public double PCT_TARGET_BASES_5000XThe fraction of all target bases achieving 5000X or greater coverage. -
PCT_TARGET_BASES_10000X
public double PCT_TARGET_BASES_10000XThe fraction of all target bases achieving 10000X or greater coverage. -
PCT_TARGET_BASES_25000X
public double PCT_TARGET_BASES_25000XThe fraction of all target bases achieving 25000X or greater coverage. -
PCT_TARGET_BASES_50000X
public double PCT_TARGET_BASES_50000XThe fraction of all target bases achieving 50000X or greater coverage. -
PCT_TARGET_BASES_100000X
public double PCT_TARGET_BASES_100000XThe fraction of all target bases achieving 100000X or greater coverage. -
AT_DROPOUT
public double AT_DROPOUTA measure of how undercovered <= 50% GC regions are relative to the mean. For each GC bin [0..50] we calculate a = % of target territory, and b = % of aligned reads aligned to these targets. AT DROPOUT is then abs(sum(a-b when a-b < 0)). E.g. if the value is 5% this implies that 5% of total reads that should have mapped to GC<=50% regions mapped elsewhere. -
GC_DROPOUT
public double GC_DROPOUTA measure of how undercovered >= 50% GC regions are relative to the mean. For each GC bin [50..100] we calculate a = % of target territory, and b = % of aligned reads aligned to these targets. GC DROPOUT is then abs(sum(a-b when a-b < 0)). E.g. if the value is 5% this implies that 5% of total reads that should have mapped to GC>=50% regions mapped elsewhere. -
HET_SNP_SENSITIVITY
public double HET_SNP_SENSITIVITYThe theoretical HET SNP sensitivity. -
HET_SNP_Q
public double HET_SNP_QThe Phred Scaled Q Score of the theoretical HET SNP sensitivity.
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Constructor Details
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PanelMetricsBase
public PanelMetricsBase()
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