CollectWgsMetrics.WgsMetrics (PICARD JDK API Documentation)

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

Direct Known Subclasses:

CollectRawWgsMetrics.RawWgsMetrics, CollectWgsMetricsFromQuerySorted.QuerySortedSeqMetrics, CollectWgsMetricsFromSampledSites.SampledWgsMetrics, CollectWgsMetricsWithNonZeroCoverage.WgsMetricsWithNonZeroCoverage

Enclosing class:

CollectWgsMetrics
```
public static class CollectWgsMetrics.WgsMetrics
extends htsjdk.samtools.metrics.MetricBase
```
Metrics for evaluating the performance of whole genome sequencing experiments.

Field Summary

Fields
Modifier and Type	Field and Description
`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.
`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_BASEQ` The fraction of aligned bases that were filtered out because they were of low base quality (default is < 20).
`double`	`PCT_EXC_CAPPED` The fraction of aligned bases that were filtered out because they would have raised coverage above the capped value (default cap = 250x).
`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 (default is < 20).
`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.

Constructor Summary

Constructors
Constructor and Description

WgsMetrics()

Constructors
Constructor and Description
`WgsMetrics()`

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
  - 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_MAPQ
```
public double PCT_EXC_MAPQ
```
    The fraction of aligned bases that were filtered out because they were in reads with low mapping quality (default is < 20).
  - 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 (default is < 20).
  - 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 the capped value (default cap = 250x).
  - 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()
```

Class CollectWgsMetrics.WgsMetrics

Field Summary

Constructor Summary

Method Summary

Methods inherited from class htsjdk.samtools.metrics.MetricBase

Methods inherited from class java.lang.Object

Field Detail

GENOME_TERRITORY

MEAN_COVERAGE

SD_COVERAGE

MEDIAN_COVERAGE

MAD_COVERAGE

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