HsMetrics (PICARD JDK API Documentation)

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.
Author:

Tim Fennell

Field Summary

Fields
Modifier and Type	Field and Description
`double`	`AT_DROPOUT` A measure of how undercovered <= 50% GC regions are relative to the mean.
`double`	`BAIT_DESIGN_EFFICIENCY` Target terrirtoy / bait territory.
`java.lang.String`	`BAIT_SET` The name of the bait set used in the hybrid selection.
`long`	`BAIT_TERRITORY` The number of bases which have one or more baits on top of them.
`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.
`java.lang.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.
`double`	`MEAN_BAIT_COVERAGE` The mean coverage of all baits in the experiment.
`double`	`MEAN_TARGET_COVERAGE` The mean coverage of targets.
`double`	`MEDIAN_TARGET_COVERAGE` The median coverage of targets.
`long`	`NEAR_BAIT_BASES` The number of PF aligned bases that mapped to within a fixed interval of a baited region, but not on a baited region.
`long`	`OFF_BAIT_BASES` The number of PF aligned bases that mapped to neither on or near a bait.
`long`	`ON_BAIT_BASES` The number of PF aligned bases that mapped to a baited region of the genome.
`double`	`ON_BAIT_VS_SELECTED` The percentage of on+near bait bases that are on as opposed to near.
`long`	`ON_TARGET_BASES` The number of PF aligned bases that 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 percentage of aligned PF bases that mapped neither on or near a bait.
`double`	`PCT_PF_READS` PF reads / total reads.
`double`	`PCT_PF_UQ_READS` PF Unique Reads / Total Reads.
`double`	`PCT_PF_UQ_READS_ALIGNED` PF Reads Aligned / PF Reads.
`double`	`PCT_SELECTED_BASES` On+Near Bait Bases / PF Bases Aligned.
`double`	`PCT_TARGET_BASES_100X` The percentage of all target bases achieving 100X or greater coverage.
`double`	`PCT_TARGET_BASES_10X` The percentage of all target bases achieving 10X or greater coverage.
`double`	`PCT_TARGET_BASES_1X` The percentage of all target bases achieving 1X or greater coverage.
`double`	`PCT_TARGET_BASES_20X` The percentage of all target bases achieving 20X or greater coverage.
`double`	`PCT_TARGET_BASES_2X` The percentage of all target bases achieving 2X or greater coverage.
`double`	`PCT_TARGET_BASES_30X` The percentage of all target bases achieving 30X or greater coverage.
`double`	`PCT_TARGET_BASES_40X` The percentage of all target bases achieving 40X or greater coverage.
`double`	`PCT_TARGET_BASES_50X` The percentage 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 the PF bases available.
`long`	`PF_BASES_ALIGNED` The number of PF unique bases that are aligned with mapping score > 0 to the reference genome.
`long`	`PF_READS` The 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 aligned reads that are mapped to a reference base.
`long`	`PF_UQ_READS_ALIGNED` The number of PF unique reads that are aligned with mapping score > 0 to the reference genome.
`long`	`TARGET_TERRITORY` The unique number of target bases in the experiment where target is usually exons etc.
`long`	`TOTAL_READS` The total number of reads in the SAM or BAM file examine.
`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 and Description

HsMetrics()

Constructors
Constructor and 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 java.lang.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 have one or more baits on top of them.
  - TARGET_TERRITORY
```
public long TARGET_TERRITORY
```
    The unique number of target bases in the experiment where target is usually exons etc.
  - BAIT_DESIGN_EFFICIENCY
```
public double BAIT_DESIGN_EFFICIENCY
```
    Target terrirtoy / bait territory. 1 == perfectly efficient, 0.5 = half of baited bases are not target.
  - TOTAL_READS
```
public long TOTAL_READS
```
    The total number of reads in the SAM or BAM file examine.
  - PF_READS
```
public long PF_READS
```
    The 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
```
    PF reads / total reads. The percent of reads passing filter.
  - PCT_PF_UQ_READS
```
public double PCT_PF_UQ_READS
```
    PF Unique Reads / Total Reads.
  - 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.
  - PCT_PF_UQ_READS_ALIGNED
```
public double PCT_PF_UQ_READS_ALIGNED
```
    PF Reads Aligned / PF Reads.
  - PF_BASES_ALIGNED
```
public long PF_BASES_ALIGNED
```
    The number of PF unique 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 bases in the PF aligned reads that are mapped to a reference base. Accounts for clipping and gaps.
  - ON_BAIT_BASES
```
public long ON_BAIT_BASES
```
    The number of PF aligned bases that mapped to a baited region of the genome.
  - NEAR_BAIT_BASES
```
public long NEAR_BAIT_BASES
```
    The number of PF aligned bases that mapped to within a fixed interval of a baited region, but not on a baited region.
  - OFF_BAIT_BASES
```
public long OFF_BAIT_BASES
```
    The number of PF aligned bases that mapped to neither on or near a bait.
  - ON_TARGET_BASES
```
public long ON_TARGET_BASES
```
    The number of PF aligned bases that mapped to a targeted region of the genome.
  - PCT_SELECTED_BASES
```
public double PCT_SELECTED_BASES
```
    On+Near Bait Bases / PF Bases Aligned.
  - PCT_OFF_BAIT
```
public double PCT_OFF_BAIT
```
    The percentage of aligned PF bases that mapped neither on or near a bait.
  - ON_BAIT_VS_SELECTED
```
public double ON_BAIT_VS_SELECTED
```
    The percentage of on+near bait bases that are on as opposed to near.
  - 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 targets.
  - MEDIAN_TARGET_COVERAGE
```
public double MEDIAN_TARGET_COVERAGE
```
    The median coverage of targets.
  - 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 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 percentage of all target bases achieving 1X or greater coverage.
  - PCT_TARGET_BASES_2X
```
public double PCT_TARGET_BASES_2X
```
    The percentage of all target bases achieving 2X or greater coverage.
  - PCT_TARGET_BASES_10X
```
public double PCT_TARGET_BASES_10X
```
    The percentage of all target bases achieving 10X or greater coverage.
  - PCT_TARGET_BASES_20X
```
public double PCT_TARGET_BASES_20X
```
    The percentage of all target bases achieving 20X or greater coverage.
  - PCT_TARGET_BASES_30X
```
public double PCT_TARGET_BASES_30X
```
    The percentage of all target bases achieving 30X or greater coverage.
  - PCT_TARGET_BASES_40X
```
public double PCT_TARGET_BASES_40X
```
    The percentage of all target bases achieving 40X or greater coverage.
  - PCT_TARGET_BASES_50X
```
public double PCT_TARGET_BASES_50X
```
    The percentage of all target bases achieving 50X or greater coverage.
  - PCT_TARGET_BASES_100X
```
public double PCT_TARGET_BASES_100X
```
    The percentage of all target bases achieving 100X or greater coverage.
  - HS_LIBRARY_SIZE
```
public java.lang.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

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