TargetMetrics (picard 2.18.2 API)

java.lang.Object
- htsjdk.samtools.metrics.MetricBase
- - picard.metrics.MultilevelMetrics
  - - picard.analysis.directed.TargetMetrics

```
public class TargetMetrics
extends MultilevelMetrics
```
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

Fields
Modifier and Type	Field	Description
`double`	`AT_DROPOUT`	A measure of how undercovered <= 50% GC regions are relative to the mean.
`double`	`FOLD_80_BASE_PENALTY`	The fold over-coverage necessary to raise 80% of bases in "non-zero-cvg" targets to the mean coverage level in those targets.
`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`	`GC_DROPOUT`	A measure of how undercovered >= 50% GC regions are relative to the mean.
`long`	`GENOME_SIZE`	The number of bases in the reference genome used for alignment.
`double`	`HET_SNP_Q`	The Phred Scaled Q Score of the theoretical HET SNP sensitivity.
`double`	`HET_SNP_SENSITIVITY`	The theoretical HET SNP sensitivity.
`long`	`MAX_TARGET_COVERAGE`	The maximum coverage of reads that mapped to target regions of an experiment.
`double`	`MEAN_PROBE_COVERAGE`	The mean coverage of all probes in the experiment, ON_PROBE_BASES/PROBE_TERRITORY.
`double`	`MEAN_TARGET_COVERAGE`	The mean coverage of targets.
`double`	`MEDIAN_TARGET_COVERAGE`	The median coverage of targets.
`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 baited 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).
`long`	`ON_TARGET_BASES`	The number of PF aligned bases that mapped to a targeted region of the genome.
`long`	`ON_TARGET_FROM_PAIR_BASES`	The number of PF aligned bases that are mapped in pair to a targeted region of the genome.
`double`	`PCT_EXC_BASEQ`	The fraction of aligned bases that were filtered out because they were of low base quality.
`double`	`PCT_EXC_DUPE`	The fraction of aligned bases that were filtered out because they were in reads marked as duplicates.
`double`	`PCT_EXC_MAPQ`	The fraction of aligned bases that were filtered out because they were in reads with low mapping quality.
`double`	`PCT_EXC_OFF_TARGET`	The fraction of aligned bases that were filtered out because they did not align over a target base.
`double`	`PCT_EXC_OVERLAP`	The fraction of aligned bases that were filtered out because they were the second observation from an insert with overlapping reads.
`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_PF_READS`	The fraction of reads passing filter, PF_READS/TOTAL_READS.
`double`	`PCT_PF_UQ_READS`	The fraction of unique reads passing filter, PF_UNIQUE_READS/TOTAL_READS.
`double`	`PCT_PF_UQ_READS_ALIGNED`	The fraction of unique reads passing filter that align to the reference, PF_UQ_READS_ALIGNED/PF_UNIQUE_READS.
`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).
`double`	`PCT_TARGET_BASES_100X`	The fraction of all target bases achieving 100X or greater coverage.
`double`	`PCT_TARGET_BASES_10X`	The fraction of all target bases achieving 10X or greater coverage.
`double`	`PCT_TARGET_BASES_1X`	The fraction of all target bases achieving 1X or greater coverage.
`double`	`PCT_TARGET_BASES_20X`	The fraction of all target bases achieving 20X or greater coverage.
`double`	`PCT_TARGET_BASES_2X`	The fraction of all target bases achieving 2X or greater coverage.
`double`	`PCT_TARGET_BASES_30X`	The fraction of all target bases achieving 30X or greater coverage.
`double`	`PCT_TARGET_BASES_40X`	The fraction of all target bases achieving 40X or greater coverage.
`double`	`PCT_TARGET_BASES_50X`	The fraction of all target bases achieving 50X or greater coverage.
`long`	`PF_BASES`	The number of bases in the PF_READS of a SAM or BAM file
`long`	`PF_BASES_ALIGNED`	The number of PF_BASES that are aligned with mapping score > 0 to the reference genome.
`long`	`PF_READS`	The number of passing filter reads (PF).
`long`	`PF_SELECTED_PAIRS`	Tracks the number of read pairs that we see that are PF (used to calculate library size)
`long`	`PF_SELECTED_UNIQUE_PAIRS`	Tracks the number of unique PF_SELECTED_PAIRS we see (used to calc library size)
`long`	`PF_UNIQUE_READS`	The number of PF_READS that are not marked as duplicates.
`long`	`PF_UQ_BASES_ALIGNED`	The number of PF unique bases that are aligned with mapping score > 0 to the reference genome.
`long`	`PF_UQ_READS_ALIGNED`	The number of PF_UNIQUE_READS that are aligned with mapping score > 0 to the reference genome.
`String`	`PROBE_SET`	The name of the PROBE_SET (BAIT_SET, AMPLICON_SET, ...) used in this metrics collection run
`long`	`PROBE_TERRITORY`	The number of unique bases covered by the intervals of all probes in the probe set
`long`	`TARGET_TERRITORY`	The number of unique bases covered by the intervals of all targets that should be covered
`long`	`TOTAL_READS`	The total number of reads in the SAM or BAM file examined.
`double`	`ZERO_CVG_TARGETS_PCT`	The fraction of targets that did not reach coverage=1 over any base.

Fields inherited from class picard.metrics.MultilevelMetrics
LIBRARY, READ_GROUP, SAMPLE

Constructor Summary

Constructors
Constructor Description

TargetMetrics()

Constructors
Constructor	Description
`TargetMetrics()`

Method Summary
- Methods inherited from class htsjdk.samtools.metrics.MetricBase
  equals, hashCode, toString
- Methods inherited from class java.lang.Object
  clone, finalize, getClass, notify, notifyAll, wait, wait, wait

- Field Detail
  - PROBE_SET
```
public String PROBE_SET
```
    The name of the PROBE_SET (BAIT_SET, AMPLICON_SET, ...) used in this metrics collection run
  - PROBE_TERRITORY
```
public long PROBE_TERRITORY
```
    The number of unique bases covered by the intervals of all probes in the probe set
  - TARGET_TERRITORY
```
public long TARGET_TERRITORY
```
    The number of unique bases covered by the intervals of all targets that should be covered
  - GENOME_SIZE
```
public long GENOME_SIZE
```
    The number of bases in the reference genome used for alignment.
  - TOTAL_READS
```
public long TOTAL_READS
```
    The total number of reads in the SAM or BAM file examined.
  - PF_READS
```
public long PF_READS
```
    The number of passing filter reads (PF).
  - PF_BASES
```
public long PF_BASES
```
    The number of bases in the PF_READS of a SAM or BAM file
  - PF_UNIQUE_READS
```
public long PF_UNIQUE_READS
```
    The number of PF_READS that are not marked as duplicates.
  - PF_SELECTED_PAIRS
```
public long PF_SELECTED_PAIRS
```
    Tracks the number of read pairs that we see that are PF (used to calculate library size)
  - PF_SELECTED_UNIQUE_PAIRS
```
public long PF_SELECTED_UNIQUE_PAIRS
```
    Tracks the number of unique PF_SELECTED_PAIRS we see (used to calc library size)
  - PF_UQ_READS_ALIGNED
```
public long PF_UQ_READS_ALIGNED
```
    The number of PF_UNIQUE_READS that are aligned with mapping score > 0 to the reference genome.
  - PF_BASES_ALIGNED
```
public long PF_BASES_ALIGNED
```
    The number of PF_BASES that are aligned with mapping score > 0 to the reference genome.
  - PF_UQ_BASES_ALIGNED
```
public long PF_UQ_BASES_ALIGNED
```
    The number of PF unique bases that are aligned with mapping score > 0 to the reference genome.
  - ON_PROBE_BASES
```
public long ON_PROBE_BASES
```
    The number of PF aligned probed bases that mapped to a baited region of the genome.
  - 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 baited region.
  - OFF_PROBE_BASES
```
public long OFF_PROBE_BASES
```
    The number of PF aligned bases that mapped to neither on or near a probe.
  - ON_TARGET_BASES
```
public long ON_TARGET_BASES
```
    The number of PF aligned bases that mapped to a targeted region of the genome.
  - ON_TARGET_FROM_PAIR_BASES
```
public long ON_TARGET_FROM_PAIR_BASES
```
    The number of PF aligned bases that are mapped in pair to a targeted region of the genome.
  - PCT_PF_READS
```
public double PCT_PF_READS
```
    The fraction of reads passing filter, PF_READS/TOTAL_READS.
  - PCT_PF_UQ_READS
```
public double PCT_PF_UQ_READS
```
    The fraction of unique reads passing filter, PF_UNIQUE_READS/TOTAL_READS.
  - PCT_PF_UQ_READS_ALIGNED
```
public double PCT_PF_UQ_READS_ALIGNED
```
    The fraction of unique reads passing filter that align to the reference, PF_UQ_READS_ALIGNED/PF_UNIQUE_READS.
  - 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).
  - 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).
  - 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).
  - MEAN_PROBE_COVERAGE
```
public double MEAN_PROBE_COVERAGE
```
    The mean coverage of all probes in the experiment, ON_PROBE_BASES/PROBE_TERRITORY.
  - 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)
  - MEAN_TARGET_COVERAGE
```
public double MEAN_TARGET_COVERAGE
```
    The mean coverage of targets.
  - MEDIAN_TARGET_COVERAGE
```
public double MEDIAN_TARGET_COVERAGE
```
    The median coverage of targets.
  - MAX_TARGET_COVERAGE
```
public long MAX_TARGET_COVERAGE
```
    The maximum coverage of reads that mapped to target regions of an experiment.
  - ZERO_CVG_TARGETS_PCT
```
public double ZERO_CVG_TARGETS_PCT
```
    The fraction of targets that did not reach coverage=1 over any base.
  - PCT_EXC_DUPE
```
public double PCT_EXC_DUPE
```
    The fraction of aligned bases that were filtered out because they were in reads marked as duplicates.
  - PCT_EXC_MAPQ
```
public double PCT_EXC_MAPQ
```
    The fraction of aligned bases that were filtered out because they were in reads with low mapping quality.
  - PCT_EXC_BASEQ
```
public double PCT_EXC_BASEQ
```
    The fraction of aligned bases that were filtered out because they were of low base quality.
  - PCT_EXC_OVERLAP
```
public double PCT_EXC_OVERLAP
```
    The 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_TARGET
```
    The 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_PENALTY
```
    The 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_1X
```
    The fraction of all target bases achieving 1X or greater coverage.
  - PCT_TARGET_BASES_2X
```
public double PCT_TARGET_BASES_2X
```
    The fraction of all target bases achieving 2X or greater coverage.
  - PCT_TARGET_BASES_10X
```
public double PCT_TARGET_BASES_10X
```
    The fraction of all target bases achieving 10X or greater coverage.
  - PCT_TARGET_BASES_20X
```
public double PCT_TARGET_BASES_20X
```
    The fraction of all target bases achieving 20X or greater coverage.
  - PCT_TARGET_BASES_30X
```
public double PCT_TARGET_BASES_30X
```
    The fraction of all target bases achieving 30X or greater coverage.
  - PCT_TARGET_BASES_40X
```
public double PCT_TARGET_BASES_40X
```
    The fraction of all target bases achieving 40X or greater coverage.
  - PCT_TARGET_BASES_50X
```
public double PCT_TARGET_BASES_50X
```
    The fraction of all target bases achieving 50X or greater coverage.
  - PCT_TARGET_BASES_100X
```
public double PCT_TARGET_BASES_100X
```
    The fraction of all target bases achieving 100X or greater coverage.
  - AT_DROPOUT
```
public double AT_DROPOUT
```
    A 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_DROPOUT
```
    A 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_SENSITIVITY
```
    The theoretical HET SNP sensitivity.
  - HET_SNP_Q
```
public double HET_SNP_Q
```
    The Phred Scaled Q Score of the theoretical HET SNP sensitivity.
- Constructor Detail
  - TargetMetrics
```
public TargetMetrics()
```

Class TargetMetrics

Field Summary

Fields inherited from class picard.metrics.MultilevelMetrics

Constructor Summary

Method Summary

Methods inherited from class htsjdk.samtools.metrics.MetricBase

Methods inherited from class java.lang.Object

Field Detail

PROBE_SET

PROBE_TERRITORY

TARGET_TERRITORY

GENOME_SIZE

TOTAL_READS

PF_READS

PF_BASES

PF_UNIQUE_READS

PF_SELECTED_PAIRS

PF_SELECTED_UNIQUE_PAIRS

PF_UQ_READS_ALIGNED

PF_BASES_ALIGNED

PF_UQ_BASES_ALIGNED

ON_PROBE_BASES

NEAR_PROBE_BASES

OFF_PROBE_BASES

ON_TARGET_BASES

ON_TARGET_FROM_PAIR_BASES

PCT_PF_READS

PCT_PF_UQ_READS

PCT_PF_UQ_READS_ALIGNED

PCT_SELECTED_BASES

PCT_OFF_PROBE

ON_PROBE_VS_SELECTED

MEAN_PROBE_COVERAGE

FOLD_ENRICHMENT

MEAN_TARGET_COVERAGE

MEDIAN_TARGET_COVERAGE

MAX_TARGET_COVERAGE

ZERO_CVG_TARGETS_PCT

PCT_EXC_DUPE

PCT_EXC_MAPQ

PCT_EXC_BASEQ

PCT_EXC_OVERLAP

PCT_EXC_OFF_TARGET

FOLD_80_BASE_PENALTY

PCT_TARGET_BASES_1X

PCT_TARGET_BASES_2X

PCT_TARGET_BASES_10X

PCT_TARGET_BASES_20X

PCT_TARGET_BASES_30X

PCT_TARGET_BASES_40X

PCT_TARGET_BASES_50X

PCT_TARGET_BASES_100X

AT_DROPOUT

GC_DROPOUT

HET_SNP_SENSITIVITY

HET_SNP_Q

Constructor Detail

TargetMetrics