WgsMetrics (gatk 4.1.4.1 API)

java.lang.Object
- htsjdk.samtools.metrics.MetricBase
- - picard.analysis.MergeableMetricBase
  - - picard.analysis.WgsMetrics

Direct Known Subclasses:

CollectRawWgsMetrics.RawWgsMetrics, CollectWgsMetricsWithNonZeroCoverage.WgsMetricsWithNonZeroCoverage
```
public class WgsMetrics
extends MergeableMetricBase
```
Metrics for evaluating the performance of whole genome sequencing experiments.

Nested Class Summary
- Nested classes/interfaces inherited from class picard.analysis.MergeableMetricBase
  MergeableMetricBase.MergeByAdding, MergeableMetricBase.MergeByAssertEquals, MergeableMetricBase.MergingIsManual, MergeableMetricBase.NoMergingIsDerived, MergeableMetricBase.NoMergingKeepsValue

Field Summary

Fields
Modifier and Type	Field and Description
`protected int`	`coverageCap` The maximum depth/coverage to consider.
`long`	`GENOME_TERRITORY` The number of non-N bases in the genome reference over which coverage will be evaluated.
`double`	`HET_SNP_Q` The Phred Scaled Q Score of the theoretical HET SNP sensitivity.
`double`	`HET_SNP_SENSITIVITY` The theoretical HET SNP sensitivity.
`protected htsjdk.samtools.util.Histogram<java.lang.Integer>`	`highQualityDepthHistogram` Count of sites with a given depth of coverage.
`protected htsjdk.samtools.util.IntervalList`	`intervals` The intervals over which this metric was computed.
`double`	`MAD_COVERAGE` The median absolute deviation of coverage of the genome after all filters are applied.
`double`	`MEAN_COVERAGE` The mean coverage in bases of the genome territory, after all filters are applied.
`double`	`MEDIAN_COVERAGE` The median coverage in bases of the genome territory, after all filters are applied.
`double`	`PCT_100X` The fraction of bases that attained at least 100X sequence coverage in post-filtering bases.
`double`	`PCT_10X` The fraction of bases that attained at least 10X sequence coverage in post-filtering bases.
`double`	`PCT_15X` The fraction of bases that attained at least 15X sequence coverage in post-filtering bases.
`double`	`PCT_1X` The fraction of bases that attained at least 1X sequence coverage in post-filtering bases.
`double`	`PCT_20X` The fraction of bases that attained at least 20X sequence coverage in post-filtering bases.
`double`	`PCT_25X` The fraction of bases that attained at least 25X sequence coverage in post-filtering bases.
`double`	`PCT_30X` The fraction of bases that attained at least 30X sequence coverage in post-filtering bases.
`double`	`PCT_40X` The fraction of bases that attained at least 40X sequence coverage in post-filtering bases.
`double`	`PCT_50X` The fraction of bases that attained at least 50X sequence coverage in post-filtering bases.
`double`	`PCT_5X` The fraction of bases that attained at least 5X sequence coverage in post-filtering bases.
`double`	`PCT_60X` The fraction of bases that attained at least 60X sequence coverage in post-filtering bases.
`double`	`PCT_70X` The fraction of bases that attained at least 70X sequence coverage in post-filtering bases.
`double`	`PCT_80X` The fraction of bases that attained at least 80X sequence coverage in post-filtering bases.
`double`	`PCT_90X` The fraction of bases that attained at least 90X sequence coverage in post-filtering bases.
`double`	`PCT_EXC_ADAPTER` The fraction of aligned bases that were filtered out because they were in reads with mapping quality 0 and the looked like adapter reads.
`double`	`PCT_EXC_BASEQ` The fraction of aligned bases that were filtered out because they were of low base quality (lower than MIN_BASE_QUALITY).
`double`	`PCT_EXC_CAPPED` The fraction of aligned bases that were filtered out because they would have raised coverage above COVERAGE_CAP.
`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 (lower than MIN_MAPPING_QUALITY).
`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_EXC_TOTAL` The total fraction of aligned bases excluded due to all filters.
`double`	`PCT_EXC_UNPAIRED` The fraction of aligned bases that were filtered out because they were in reads without a mapped mate pair.
`double`	`SD_COVERAGE` The standard deviation of coverage of the genome after all filters are applied.
`protected int`	`theoreticalHetSensitivitySampleSize` The sample size used for theoretical het sensitivity.
`protected htsjdk.samtools.util.Histogram<java.lang.Integer>`	`unfilteredBaseQHistogram` The count of bases observed with a given base quality.
`protected htsjdk.samtools.util.Histogram<java.lang.Integer>`	`unfilteredDepthHistogram` Count of sites with a given depth of coverage.

Constructor Summary

Constructors
Constructor and Description
`WgsMetrics()` Create an instance of this metric that is not mergeable.
WgsMetrics(htsjdk.samtools.util.IntervalList intervals, htsjdk.samtools.util.Histogram<java.lang.Integer> highQualityDepthHistogram, htsjdk.samtools.util.Histogram<java.lang.Integer> unfilteredDepthHistogram, double pctExcludedByAdapter, double pctExcludedByMapq, double pctExcludedByDupes, double pctExcludedByPairing, double pctExcludedByBaseq, double pctExcludedByOverlap, double pctExcludedByCapping, double pctExcludeTotal, int coverageCap, htsjdk.samtools.util.Histogram<java.lang.Integer> unfilteredBaseQHistogram, int theoreticalHetSensitivitySampleSize) Create an instance of this metric that is mergeable.

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`void`	`calculateDerivedFields()` Placeholder method that will calculate the derived fields from the other ones.
`MergeableMetricBase`	`merge(MergeableMetricBase other)` Merges the various PCT_EXC_* metrics.

Methods inherited from class picard.analysis.MergeableMetricBase
canMerge, merge, mergeIfCan

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
  - intervals
```
protected htsjdk.samtools.util.IntervalList intervals
```
    The intervals over which this metric was computed.
  - highQualityDepthHistogram
```
protected final htsjdk.samtools.util.Histogram<java.lang.Integer> highQualityDepthHistogram
```
    Count of sites with a given depth of coverage. Excludes bases with quality below MINIMUM_BASE_QUALITY
  - unfilteredDepthHistogram
```
protected final htsjdk.samtools.util.Histogram<java.lang.Integer> unfilteredDepthHistogram
```
    Count of sites with a given depth of coverage. Includes all but quality 2 bases
  - unfilteredBaseQHistogram
```
protected final htsjdk.samtools.util.Histogram<java.lang.Integer> unfilteredBaseQHistogram
```
    The count of bases observed with a given base quality.
  - coverageCap
```
protected final int coverageCap
```
    The maximum depth/coverage to consider.
  - theoreticalHetSensitivitySampleSize
```
protected final int theoreticalHetSensitivitySampleSize
```
    The sample size used for theoretical het sensitivity.
  - GENOME_TERRITORY
```
public long GENOME_TERRITORY
```
    The number of non-N bases in the genome reference over which coverage will be evaluated.
  - MEAN_COVERAGE
```
public double MEAN_COVERAGE
```
    The mean coverage in bases of the genome territory, after all filters are applied.
  - SD_COVERAGE
```
public double SD_COVERAGE
```
    The standard deviation of coverage of the genome after all filters are applied.
  - MEDIAN_COVERAGE
```
public double MEDIAN_COVERAGE
```
    The median coverage in bases of the genome territory, after all filters are applied.
  - MAD_COVERAGE
```
public double MAD_COVERAGE
```
    The median absolute deviation of coverage of the genome after all filters are applied.
  - PCT_EXC_ADAPTER
```
public double PCT_EXC_ADAPTER
```
    The fraction of aligned bases that were filtered out because they were in reads with mapping quality 0 and the looked like adapter reads.
  - 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 (lower than MIN_MAPPING_QUALITY).
  - 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_UNPAIRED
```
public double PCT_EXC_UNPAIRED
```
    The fraction of aligned bases that were filtered out because they were in reads without a mapped mate pair.
  - PCT_EXC_BASEQ
```
public double PCT_EXC_BASEQ
```
    The fraction of aligned bases that were filtered out because they were of low base quality (lower than MIN_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_CAPPED
```
public double PCT_EXC_CAPPED
```
    The fraction of aligned bases that were filtered out because they would have raised coverage above COVERAGE_CAP.
  - PCT_EXC_TOTAL
```
public double PCT_EXC_TOTAL
```
    The total fraction of aligned bases excluded due to all filters.
  - PCT_1X
```
public double PCT_1X
```
    The fraction of bases that attained at least 1X sequence coverage in post-filtering bases.
  - PCT_5X
```
public double PCT_5X
```
    The fraction of bases that attained at least 5X sequence coverage in post-filtering bases.
  - PCT_10X
```
public double PCT_10X
```
    The fraction of bases that attained at least 10X sequence coverage in post-filtering bases.
  - PCT_15X
```
public double PCT_15X
```
    The fraction of bases that attained at least 15X sequence coverage in post-filtering bases.
  - PCT_20X
```
public double PCT_20X
```
    The fraction of bases that attained at least 20X sequence coverage in post-filtering bases.
  - PCT_25X
```
public double PCT_25X
```
    The fraction of bases that attained at least 25X sequence coverage in post-filtering bases.
  - PCT_30X
```
public double PCT_30X
```
    The fraction of bases that attained at least 30X sequence coverage in post-filtering bases.
  - PCT_40X
```
public double PCT_40X
```
    The fraction of bases that attained at least 40X sequence coverage in post-filtering bases.
  - PCT_50X
```
public double PCT_50X
```
    The fraction of bases that attained at least 50X sequence coverage in post-filtering bases.
  - PCT_60X
```
public double PCT_60X
```
    The fraction of bases that attained at least 60X sequence coverage in post-filtering bases.
  - PCT_70X
```
public double PCT_70X
```
    The fraction of bases that attained at least 70X sequence coverage in post-filtering bases.
  - PCT_80X
```
public double PCT_80X
```
    The fraction of bases that attained at least 80X sequence coverage in post-filtering bases.
  - PCT_90X
```
public double PCT_90X
```
    The fraction of bases that attained at least 90X sequence coverage in post-filtering bases.
  - PCT_100X
```
public double PCT_100X
```
    The fraction of bases that attained at least 100X sequence coverage in post-filtering bases.
  - 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
  - WgsMetrics
```
public WgsMetrics()
```
    Create an instance of this metric that is not mergeable.
  - WgsMetrics
```
public WgsMetrics(htsjdk.samtools.util.IntervalList intervals,
                  htsjdk.samtools.util.Histogram<java.lang.Integer> highQualityDepthHistogram,
                  htsjdk.samtools.util.Histogram<java.lang.Integer> unfilteredDepthHistogram,
                  double pctExcludedByAdapter,
                  double pctExcludedByMapq,
                  double pctExcludedByDupes,
                  double pctExcludedByPairing,
                  double pctExcludedByBaseq,
                  double pctExcludedByOverlap,
                  double pctExcludedByCapping,
                  double pctExcludeTotal,
                  int coverageCap,
                  htsjdk.samtools.util.Histogram<java.lang.Integer> unfilteredBaseQHistogram,
                  int theoreticalHetSensitivitySampleSize)
```
    Create an instance of this metric that is mergeable.
    
    Parameters:
    
    highQualityDepthHistogram - the count of genomic positions observed for each observed depth. Excludes bases with quality below MINIMUM_BASE_QUALITY.
    
    unfilteredDepthHistogram - the depth histogram that includes all but quality 2 bases.
    
    pctExcludedByAdapter - the fraction of aligned bases that were filtered out because they were in reads with 0 mapping quality that looked like adapter sequence.
    
    pctExcludedByMapq - the fraction of aligned bases that were filtered out because they were in reads with low mapping quality.
    
    pctExcludedByDupes - the fraction of aligned bases that were filtered out because they were in reads marked as duplicates.
    
    pctExcludedByPairing - the fraction of bases that were filtered out because they were in reads without a mapped mate pair.
    
    pctExcludedByBaseq - the fraction of aligned bases that were filtered out because they were of low base quality.
    
    pctExcludedByOverlap - the fraction of aligned bases that were filtered out because they were the second observation from an insert with overlapping reads.
    
    pctExcludedByCapping - the fraction of aligned bases that were filtered out because they would have raised coverage above the capped value.
    
    pctExcludeTotal - the fraction of bases excluded across all filters.
    
    coverageCap - Treat positions with coverage exceeding this value as if they had coverage at this value.
    
    unfilteredBaseQHistogram - the count of bases observed with a given quality. Includes all but quality 2 bases.
    
    theoreticalHetSensitivitySampleSize - the sample size used for theoretical het sensitivity sampling.
- Method Detail
  - merge
```
public MergeableMetricBase merge(MergeableMetricBase other)
```
    Merges the various PCT_EXC_* metrics.
    
    Overrides:
    
    merge in class MergeableMetricBase
    
    Parameters:
    
    other - metric to merge into this one.
    
    Returns:
    
    result of merging, also known as "this"
  - calculateDerivedFields
```
public void calculateDerivedFields()
```
    Description copied from class: MergeableMetricBase
    
    Placeholder method that will calculate the derived fields from the other ones. Classes that are derived from non-trivial derived classes should consider calling super.calculateDerivedFields() as well. Fields whose value will change due to this method should be annotated with NoMergingKeepsValue.
    
    Overrides:
    
    calculateDerivedFields in class MergeableMetricBase

Class WgsMetrics

Nested Class Summary

Nested classes/interfaces inherited from class picard.analysis.MergeableMetricBase

Field Summary

Constructor Summary

Method Summary

Methods inherited from class picard.analysis.MergeableMetricBase

Methods inherited from class htsjdk.samtools.metrics.MetricBase

Methods inherited from class java.lang.Object

Field Detail

intervals

highQualityDepthHistogram

unfilteredDepthHistogram

unfilteredBaseQHistogram

coverageCap

theoreticalHetSensitivitySampleSize

GENOME_TERRITORY

MEAN_COVERAGE

SD_COVERAGE

MEDIAN_COVERAGE

MAD_COVERAGE

PCT_EXC_ADAPTER

PCT_EXC_MAPQ

PCT_EXC_DUPE

PCT_EXC_UNPAIRED

PCT_EXC_BASEQ

PCT_EXC_OVERLAP

PCT_EXC_CAPPED

PCT_EXC_TOTAL

PCT_1X

PCT_5X

PCT_10X

PCT_15X

PCT_20X

PCT_25X

PCT_30X

PCT_40X

PCT_50X

PCT_60X

PCT_70X

PCT_80X

PCT_90X

PCT_100X

HET_SNP_SENSITIVITY

HET_SNP_Q

Constructor Detail

WgsMetrics

WgsMetrics

Method Detail

merge

calculateDerivedFields