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

```
public class HsMetrics
extends MultilevelMetrics
```
Metrics generated by CollectHsMetrics for the analysis of target-capture sequencing experiments. The metrics in this class fall broadly into three categories:
- Basic sequencing metrics that are either generated as a baseline against which to evaluate other metrics or because they are used in the calculation of other metrics. This includes things like the genome size, the number of reads, the number of aligned reads etc.
- Metrics that are intended for evaluating the performance of the wet-lab assay that generated the data. This group includes metrics like the number of bases mapping on/off/near baits, %selected, fold 80 base penalty, hs library size and the hs penalty metrics. These metrics are calculated prior to some of the filters are applied (e.g. low mapping quality reads, low base quality bases and bases overlapping in the middle of paired-end reads are all counted).
- Metrics for assessing target coverage as a proxy for how well the data is likely to perform in downstream applications like variant calling. This group includes metrics like mean target coverage, the percentage of bases reaching various coverage levels, and the percentage of bases excluded by various filters. These metrics are computed using the strictest subset of the data, after all filters have been applied.

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`	`BAIT_DESIGN_EFFICIENCY`	The ratio of TARGET_TERRITORY/BAIT_TERRITORY.
`String`	`BAIT_SET`	The name of the bait set used in the hybrid selection.
`long`	`BAIT_TERRITORY`	The number of bases which are localized to one or more baits.
`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 baited region has been amplified above genomic background.
`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`	`HS_LIBRARY_SIZE`	The estimated number of unique molecules in the selected part of the library.
`double`	`HS_PENALTY_100X`	The "hybrid selection penalty" incurred to get 80% of target bases to 100X.
`double`	`HS_PENALTY_10X`	The "hybrid selection penalty" incurred to get 80% of target bases to 10X.
`double`	`HS_PENALTY_20X`	The "hybrid selection penalty" incurred to get 80% of target bases to 20X.
`double`	`HS_PENALTY_30X`	The "hybrid selection penalty" incurred to get 80% of target bases to 30X.
`double`	`HS_PENALTY_40X`	The "hybrid selection penalty" incurred to get 80% of target bases to 40X.
`double`	`HS_PENALTY_50X`	The "hybrid selection penalty" incurred to get 80% of target bases to 50X.
`long`	`MAX_TARGET_COVERAGE`	The maximum coverage of reads that mapped to target regions of an experiment.
`double`	`MEAN_BAIT_COVERAGE`	The mean coverage of all baits in the experiment.
`double`	`MEAN_TARGET_COVERAGE`	The mean coverage of a target region.
`double`	`MEDIAN_TARGET_COVERAGE`	The median coverage of a target region.
`long`	`NEAR_BAIT_BASES`	The number of PF_BASES_ALIGNED that are mapped to within a fixed interval containing a baited region, but not within the baited section per se.
`long`	`OFF_BAIT_BASES`	The number of PF_BASES_ALIGNED that are mapped away from any baited region.
`long`	`ON_BAIT_BASES`	The number of PF_BASES_ALIGNED that are mapped to the baited regions of the genome.
`double`	`ON_BAIT_VS_SELECTED`	The fraction of bases on or near baits that are covered by baits, ON_BAIT_BASES/(ON_BAIT_BASES + NEAR_BAIT_BASES).
`long`	`ON_TARGET_BASES`	The number of PF_BASES_ALIGNED that are mapped 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_BAIT`	The fraction of PF_BASES_ALIGNED that are mapped away from any baited region, OFF_BAIT_BASES/PF_BASES_ALIGNED.
`double`	`PCT_PF_READS`	The fraction of reads passing the vendor's filter, PF_READS/TOTAL_READS.
`double`	`PCT_PF_UQ_READS`	The fraction of PF_UNIQUE_READS from the TOTAL_READS, PF_UNIQUE_READS/TOTAL_READS.
`double`	`PCT_PF_UQ_READS_ALIGNED`	The fraction of PF_UQ_READS_ALIGNED from the total number of PF reads.
`double`	`PCT_SELECTED_BASES`	The fraction of PF_BASES_ALIGNED located on or near a baited region (ON_BAIT_BASES + NEAR_BAIT_BASES)/PF_BASES_ALIGNED.
`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.
`double`	`PCT_USABLE_BASES_ON_BAIT`	The number of aligned, de-duped, on-bait bases out of the PF bases available.
`double`	`PCT_USABLE_BASES_ON_TARGET`	The number of aligned, de-duped, on-target bases out of all of the PF bases available.
`long`	`PF_BASES_ALIGNED`	The number of PF unique bases that are aligned to the reference genome with mapping scores > 0.
`long`	`PF_READS`	The total number of reads that pass the vendor's filter.
`long`	`PF_UNIQUE_READS`	The number of PF reads that are not marked as duplicates.
`long`	`PF_UQ_BASES_ALIGNED`	The number of bases in the PF_UQ_READS_ALIGNED reads.
`long`	`PF_UQ_READS_ALIGNED`	The number of PF_UNIQUE_READS that aligned to the reference genome with a mapping score > 0.
`long`	`TARGET_TERRITORY`	The unique number of target bases in the experiment, where the target sequence is usually exons etc.
`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

HsMetrics()

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
  - BAIT_SET
```
public String BAIT_SET
```
    The name of the bait set used in the hybrid selection.
  - GENOME_SIZE
```
public long GENOME_SIZE
```
    The number of bases in the reference genome used for alignment.
  - BAIT_TERRITORY
```
public long BAIT_TERRITORY
```
    The number of bases which are localized to one or more baits.
  - TARGET_TERRITORY
```
public long TARGET_TERRITORY
```
    The unique number of target bases in the experiment, where the target sequence is usually exons etc.
  - BAIT_DESIGN_EFFICIENCY
```
public double BAIT_DESIGN_EFFICIENCY
```
    The ratio of TARGET_TERRITORY/BAIT_TERRITORY. A value of 1 indicates a perfect design efficiency, while a valud of 0.5 indicates that half of bases within the bait region are not within the target region.
  - 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 total number of reads that pass the vendor's filter.
  - PF_UNIQUE_READS
```
public long PF_UNIQUE_READS
```
    The number of PF reads that are not marked as duplicates.
  - PCT_PF_READS
```
public double PCT_PF_READS
```
    The fraction of reads passing the vendor's filter, PF_READS/TOTAL_READS.
  - PCT_PF_UQ_READS
```
public double PCT_PF_UQ_READS
```
    The fraction of PF_UNIQUE_READS from the TOTAL_READS, PF_UNIQUE_READS/TOTAL_READS.
  - PF_UQ_READS_ALIGNED
```
public long PF_UQ_READS_ALIGNED
```
    The number of PF_UNIQUE_READS that aligned to the reference genome with a mapping score > 0.
  - PCT_PF_UQ_READS_ALIGNED
```
public double PCT_PF_UQ_READS_ALIGNED
```
    The fraction of PF_UQ_READS_ALIGNED from the total number of PF reads.
  - PF_BASES_ALIGNED
```
public long PF_BASES_ALIGNED
```
    The number of PF unique bases that are aligned to the reference genome with mapping scores > 0.
  - PF_UQ_BASES_ALIGNED
```
public long PF_UQ_BASES_ALIGNED
```
    The number of bases in the PF_UQ_READS_ALIGNED reads. Accounts for clipping and gaps.
  - ON_BAIT_BASES
```
public long ON_BAIT_BASES
```
    The number of PF_BASES_ALIGNED that are mapped to the baited regions of the genome.
  - NEAR_BAIT_BASES
```
public long NEAR_BAIT_BASES
```
    The number of PF_BASES_ALIGNED that are mapped to within a fixed interval containing a baited region, but not within the baited section per se.
  - OFF_BAIT_BASES
```
public long OFF_BAIT_BASES
```
    The number of PF_BASES_ALIGNED that are mapped away from any baited region.
  - ON_TARGET_BASES
```
public long ON_TARGET_BASES
```
    The number of PF_BASES_ALIGNED that are mapped to a targeted region of the genome.
  - PCT_SELECTED_BASES
```
public double PCT_SELECTED_BASES
```
    The fraction of PF_BASES_ALIGNED located on or near a baited region (ON_BAIT_BASES + NEAR_BAIT_BASES)/PF_BASES_ALIGNED.
  - PCT_OFF_BAIT
```
public double PCT_OFF_BAIT
```
    The fraction of PF_BASES_ALIGNED that are mapped away from any baited region, OFF_BAIT_BASES/PF_BASES_ALIGNED.
  - ON_BAIT_VS_SELECTED
```
public double ON_BAIT_VS_SELECTED
```
    The fraction of bases on or near baits that are covered by baits, ON_BAIT_BASES/(ON_BAIT_BASES + NEAR_BAIT_BASES).
  - MEAN_BAIT_COVERAGE
```
public double MEAN_BAIT_COVERAGE
```
    The mean coverage of all baits in the experiment.
  - MEAN_TARGET_COVERAGE
```
public double MEAN_TARGET_COVERAGE
```
    The mean coverage of a target region.
  - MEDIAN_TARGET_COVERAGE
```
public double MEDIAN_TARGET_COVERAGE
```
    The median coverage of a target region.
  - MAX_TARGET_COVERAGE
```
public long MAX_TARGET_COVERAGE
```
    The maximum coverage of reads that mapped to target regions of an experiment.
  - PCT_USABLE_BASES_ON_BAIT
```
public double PCT_USABLE_BASES_ON_BAIT
```
    The number of aligned, de-duped, on-bait bases out of the PF bases available.
  - PCT_USABLE_BASES_ON_TARGET
```
public double PCT_USABLE_BASES_ON_TARGET
```
    The number of aligned, de-duped, on-target bases out of all of the PF bases available.
  - FOLD_ENRICHMENT
```
public double FOLD_ENRICHMENT
```
    The fold by which the baited region has been amplified above genomic background.
  - 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.
  - HS_LIBRARY_SIZE
```
public Long HS_LIBRARY_SIZE
```
    The estimated number of unique molecules in the selected part of the library.
  - HS_PENALTY_10X
```
public double HS_PENALTY_10X
```
    The "hybrid selection penalty" incurred to get 80% of target bases to 10X. This metric should be interpreted as: if I have a design with 10 megabases of target, and want to get 10X coverage I need to sequence until PF_ALIGNED_BASES = 10^7 * 10 * HS_PENALTY_10X.
  - HS_PENALTY_20X
```
public double HS_PENALTY_20X
```
    The "hybrid selection penalty" incurred to get 80% of target bases to 20X. This metric should be interpreted as: if I have a design with 10 megabases of target, and want to get 20X coverage I need to sequence until PF_ALIGNED_BASES = 10^7 * 20 * HS_PENALTY_20X.
  - HS_PENALTY_30X
```
public double HS_PENALTY_30X
```
    The "hybrid selection penalty" incurred to get 80% of target bases to 30X. This metric should be interpreted as: if I have a design with 10 megabases of target, and want to get 30X coverage I need to sequence until PF_ALIGNED_BASES = 10^7 * 30 * HS_PENALTY_30X.
  - HS_PENALTY_40X
```
public double HS_PENALTY_40X
```
    The "hybrid selection penalty" incurred to get 80% of target bases to 40X. This metric should be interpreted as: if I have a design with 10 megabases of target, and want to get 40X coverage I need to sequence until PF_ALIGNED_BASES = 10^7 * 40 * HS_PENALTY_40X.
  - HS_PENALTY_50X
```
public double HS_PENALTY_50X
```
    The "hybrid selection penalty" incurred to get 80% of target bases to 50X. This metric should be interpreted as: if I have a design with 10 megabases of target, and want to get 50X coverage I need to sequence until PF_ALIGNED_BASES = 10^7 * 50 * HS_PENALTY_50X.
  - HS_PENALTY_100X
```
public double HS_PENALTY_100X
```
    The "hybrid selection penalty" incurred to get 80% of target bases to 100X. This metric should be interpreted as: if I have a design with 10 megabases of target, and want to get 100X coverage I need to sequence until PF_ALIGNED_BASES = 10^7 * 100 * HS_PENALTY_100X.
  - 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
  - HsMetrics
```
public HsMetrics()
```

Class HsMetrics

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

BAIT_SET

GENOME_SIZE

BAIT_TERRITORY

TARGET_TERRITORY

BAIT_DESIGN_EFFICIENCY

TOTAL_READS

PF_READS

PF_UNIQUE_READS

PCT_PF_READS

PCT_PF_UQ_READS

PF_UQ_READS_ALIGNED

PCT_PF_UQ_READS_ALIGNED

PF_BASES_ALIGNED

PF_UQ_BASES_ALIGNED

ON_BAIT_BASES

NEAR_BAIT_BASES

OFF_BAIT_BASES

ON_TARGET_BASES

PCT_SELECTED_BASES

PCT_OFF_BAIT

ON_BAIT_VS_SELECTED

MEAN_BAIT_COVERAGE

MEAN_TARGET_COVERAGE

MEDIAN_TARGET_COVERAGE

MAX_TARGET_COVERAGE

PCT_USABLE_BASES_ON_BAIT

PCT_USABLE_BASES_ON_TARGET

FOLD_ENRICHMENT

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

HS_LIBRARY_SIZE

HS_PENALTY_10X

HS_PENALTY_20X

HS_PENALTY_30X

HS_PENALTY_40X

HS_PENALTY_50X

HS_PENALTY_100X

AT_DROPOUT

GC_DROPOUT

HET_SNP_SENSITIVITY

HET_SNP_Q

Constructor Detail

HsMetrics