DuplicationMetrics (gatk 4.1.9.0 API)

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

Direct Known Subclasses:

GATKDuplicationMetrics
```
public class DuplicationMetrics
extends MergeableMetricBase
```
Metrics that are calculated during the process of marking duplicates within a stream of SAMRecords.

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
`java.lang.Long`	`ESTIMATED_LIBRARY_SIZE` The estimated number of unique molecules in the library based on PE duplication.
`java.lang.String`	`LIBRARY` The library on which the duplicate marking was performed.
`java.lang.Double`	`PERCENT_DUPLICATION` The fraction of mapped sequence that is marked as duplicate.
`long`	`READ_PAIR_DUPLICATES` The number of read pairs that were marked as duplicates.
`long`	`READ_PAIR_OPTICAL_DUPLICATES` The number of read pairs duplicates that were caused by optical duplication.
`long`	`READ_PAIRS_EXAMINED` The number of mapped read pairs examined.
`long`	`SECONDARY_OR_SUPPLEMENTARY_RDS` The number of reads that were either secondary or supplementary
`long`	`UNMAPPED_READS` The total number of unmapped reads examined.
`long`	`UNPAIRED_READ_DUPLICATES` The number of fragments that were marked as duplicates.
`long`	`UNPAIRED_READS_EXAMINED` The number of mapped reads examined which did not have a mapped mate pair, either because the read is unpaired, or the read is paired to an unmapped mate.

Constructor Summary

Constructors
Constructor and Description

DuplicationMetrics()

Constructors
Constructor and Description
`DuplicationMetrics()`

Method Summary

All Methods Static Methods Instance Methods Concrete Methods Deprecated Methods
Modifier and Type	Method and Description
`void`	`calculateDerivedFields()` Fills in the ESTIMATED_LIBRARY_SIZE based on the paired read data examined where possible and the PERCENT_DUPLICATION.
`void`	`calculateDerivedMetrics()` Deprecated.
`htsjdk.samtools.util.Histogram<java.lang.Double>`	`calculateRoiHistogram()` Calculates a histogram using the estimateRoi method to estimate the effective yield doing x sequencing for x=1..10.
`static java.lang.Long`	`estimateLibrarySize(long readPairs, long uniqueReadPairs)` Estimates the size of a library based on the number of paired end molecules observed and the number of unique pairs observed.
`static double`	`estimateRoi(long estimatedLibrarySize, double x, long pairs, long uniquePairs)` Estimates the ROI (return on investment) that one would see if a library was sequenced to x higher coverage than the observed coverage.
`static void`	`main(java.lang.String[] args)`

Methods inherited from class picard.analysis.MergeableMetricBase
canMerge, merge, 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
  - LIBRARY
```
public java.lang.String LIBRARY
```
    The library on which the duplicate marking was performed.
  - UNPAIRED_READS_EXAMINED
```
public long UNPAIRED_READS_EXAMINED
```
    The number of mapped reads examined which did not have a mapped mate pair, either because the read is unpaired, or the read is paired to an unmapped mate.
  - READ_PAIRS_EXAMINED
```
public long READ_PAIRS_EXAMINED
```
    The number of mapped read pairs examined. (Primary, non-supplemental)
  - SECONDARY_OR_SUPPLEMENTARY_RDS
```
public long SECONDARY_OR_SUPPLEMENTARY_RDS
```
    The number of reads that were either secondary or supplementary
  - UNMAPPED_READS
```
public long UNMAPPED_READS
```
    The total number of unmapped reads examined. (Primary, non-supplemental)
  - UNPAIRED_READ_DUPLICATES
```
public long UNPAIRED_READ_DUPLICATES
```
    The number of fragments that were marked as duplicates.
  - READ_PAIR_DUPLICATES
```
public long READ_PAIR_DUPLICATES
```
    The number of read pairs that were marked as duplicates.
  - READ_PAIR_OPTICAL_DUPLICATES
```
public long READ_PAIR_OPTICAL_DUPLICATES
```
    The number of read pairs duplicates that were caused by optical duplication. Value is always < READ_PAIR_DUPLICATES, which counts all duplicates regardless of source.
  - PERCENT_DUPLICATION
```
public java.lang.Double PERCENT_DUPLICATION
```
    The fraction of mapped sequence that is marked as duplicate.
  - ESTIMATED_LIBRARY_SIZE
```
public java.lang.Long ESTIMATED_LIBRARY_SIZE
```
    The estimated number of unique molecules in the library based on PE duplication.
- Constructor Detail
  - DuplicationMetrics
```
public DuplicationMetrics()
```
- Method Detail
  - calculateDerivedFields
```
public void calculateDerivedFields()
```
    Fills in the ESTIMATED_LIBRARY_SIZE based on the paired read data examined where possible and the PERCENT_DUPLICATION.
    
    Overrides:
    
    calculateDerivedFields in class MergeableMetricBase
  - calculateDerivedMetrics
```
@Deprecated
public void calculateDerivedMetrics()
```
    Deprecated.
    
    Fills in the ESTIMATED_LIBRARY_SIZE based on the paired read data examined where possible and the PERCENT_DUPLICATION.
    Deprecated, use calculateDerivedFields() instead.
  - estimateLibrarySize
```
public static java.lang.Long estimateLibrarySize(long readPairs,
                                                 long uniqueReadPairs)
```
    Estimates the size of a library based on the number of paired end molecules observed and the number of unique pairs observed.
    Based on the Lander-Waterman equation that states: C/X = 1 - exp( -N/X ) where X = number of distinct molecules in library N = number of read pairs C = number of distinct fragments observed in read pairs
  - estimateRoi
```
public static double estimateRoi(long estimatedLibrarySize,
                                 double x,
                                 long pairs,
                                 long uniquePairs)
```
    Estimates the ROI (return on investment) that one would see if a library was sequenced to x higher coverage than the observed coverage.
    
    Parameters:
    
    estimatedLibrarySize - the estimated number of molecules in the library
    
    x - the multiple of sequencing to be simulated (i.e. how many X sequencing)
    
    pairs - the number of pairs observed in the actual sequencing
    
    uniquePairs - the number of unique pairs observed in the actual sequencing
    
    Returns:
    
    a number z <= x that estimates if you had pairs*x as your sequencing then you would observe uniquePairs*z unique pairs.
  - calculateRoiHistogram
```
public htsjdk.samtools.util.Histogram<java.lang.Double> calculateRoiHistogram()
```
    Calculates a histogram using the estimateRoi method to estimate the effective yield doing x sequencing for x=1..10.
  - main
```
public static void main(java.lang.String[] args)
```

Class DuplicationMetrics

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

LIBRARY

UNPAIRED_READS_EXAMINED

READ_PAIRS_EXAMINED

SECONDARY_OR_SUPPLEMENTARY_RDS

UNMAPPED_READS

UNPAIRED_READ_DUPLICATES

READ_PAIR_DUPLICATES

READ_PAIR_OPTICAL_DUPLICATES

PERCENT_DUPLICATION

ESTIMATED_LIBRARY_SIZE

Constructor Detail

DuplicationMetrics

Method Detail

calculateDerivedFields

calculateDerivedMetrics

estimateLibrarySize

estimateRoi

calculateRoiHistogram

main