Package picard.analysis.directed
Class TargetMetrics
java.lang.Object
htsjdk.samtools.metrics.MetricBase
picard.metrics.MultilevelMetrics
picard.analysis.directed.PanelMetricsBase
picard.analysis.directed.TargetMetricsBase
picard.analysis.directed.TargetMetrics
@DocumentedFeature(groupName="Metrics",
summary="Metrics")
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.
-
Field Summary
FieldsModifier and TypeFieldDescriptiondouble
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
The mean coverage of all probes in the experiment, ON_PROBE_BASES/PROBE_TERRITORY.long
The number of PF aligned bases that mapped to within a fixed interval of a probed region, but not on a probed region.long
The number of PF aligned bases that mapped to neither on or near a probe.long
The number of PF aligned probed bases that mapped to a baited region of the genome.double
The fraction of on+near probe bases that are on as opposed to near, ON_PROBE_BASES/(ON_PROBE_BASES + NEAR_PROBE_BASES).double
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
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).The name of the PROBE_SET (BAIT_SET, AMPLICON_SET, ...) used in this metrics collection runlong
The number of unique bases covered by the intervals of all probes in the probe setFields 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
-
Constructor Summary
Constructors -
Method Summary
Methods inherited from class htsjdk.samtools.metrics.MetricBase
equals, hashCode, toString
-
Field Details
-
PROBE_SET
The name of the PROBE_SET (BAIT_SET, AMPLICON_SET, ...) used in this metrics collection run -
PROBE_TERRITORY
public long PROBE_TERRITORYThe number of unique bases covered by the intervals of all probes in the probe set -
ON_PROBE_BASES
public long ON_PROBE_BASESThe number of PF aligned probed bases that mapped to a baited region of the genome. -
NEAR_PROBE_BASES
public long NEAR_PROBE_BASESThe number of PF aligned bases that mapped to within a fixed interval of a probed region, but not on a probed region. -
OFF_PROBE_BASES
public long OFF_PROBE_BASESThe number of PF aligned bases that mapped to neither on or near a probe. -
PCT_SELECTED_BASES
public double PCT_SELECTED_BASESThe 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). -
PCT_OFF_PROBE
public double PCT_OFF_PROBEThe 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). -
ON_PROBE_VS_SELECTED
public double ON_PROBE_VS_SELECTEDThe fraction of on+near probe bases that are on as opposed to near, ON_PROBE_BASES/(ON_PROBE_BASES + NEAR_PROBE_BASES). -
MEAN_PROBE_COVERAGE
public double MEAN_PROBE_COVERAGEThe mean coverage of all probes in the experiment, ON_PROBE_BASES/PROBE_TERRITORY. -
FOLD_ENRICHMENT
public double FOLD_ENRICHMENTThe 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)
-
-
Constructor Details
-
TargetMetrics
public TargetMetrics()
-