Package picard.analysis
Class WgsMetrics
java.lang.Object
htsjdk.samtools.metrics.MetricBase
picard.analysis.MergeableMetricBase
picard.analysis.WgsMetrics
- Direct Known Subclasses:
CollectRawWgsMetrics.RawWgsMetrics
,CollectWgsMetricsWithNonZeroCoverage.WgsMetricsWithNonZeroCoverage
@DocumentedFeature(groupName="Metrics",
summary="Metrics")
public class WgsMetrics
extends MergeableMetricBase
Metrics for evaluating the performance of whole genome sequencing experiments.
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Nested Class Summary
Nested classes/interfaces inherited from class picard.analysis.MergeableMetricBase
MergeableMetricBase.MergeByAdding, MergeableMetricBase.MergeByAssertEquals, MergeableMetricBase.MergingIsManual, MergeableMetricBase.NoMergingIsDerived, MergeableMetricBase.NoMergingKeepsValue
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Field Summary
FieldsModifier and TypeFieldDescriptionprotected final int
The maximum depth/coverage to consider.double
The fold over-coverage necessary to raise 80% of bases to the mean coverage level.double
The fold over-coverage necessary to raise 90% of bases to the mean coverage level.double
The fold over-coverage necessary to raise 95% of bases to the mean coverage level.long
The number of non-N bases in the genome reference over which coverage will be evaluated.double
The Phred Scaled Q Score of the theoretical HET SNP sensitivity.double
The theoretical HET SNP sensitivity.protected final htsjdk.samtools.util.Histogram
<Integer> Count of sites with a given depth of coverage.protected htsjdk.samtools.util.IntervalList
The intervals over which this metric was computed.double
The median absolute deviation of coverage of the genome after all filters are applied.double
The mean coverage in bases of the genome territory, after all filters are applied.double
The median coverage in bases of the genome territory, after all filters are applied.double
The fraction of bases that attained at least 100X sequence coverage in post-filtering bases.double
The fraction of bases that attained at least 10X sequence coverage in post-filtering bases.double
The fraction of bases that attained at least 15X sequence coverage in post-filtering bases.double
The fraction of bases that attained at least 1X sequence coverage in post-filtering bases.double
The fraction of bases that attained at least 20X sequence coverage in post-filtering bases.double
The fraction of bases that attained at least 25X sequence coverage in post-filtering bases.double
The fraction of bases that attained at least 30X sequence coverage in post-filtering bases.double
The fraction of bases that attained at least 40X sequence coverage in post-filtering bases.double
The fraction of bases that attained at least 50X sequence coverage in post-filtering bases.double
The fraction of bases that attained at least 5X sequence coverage in post-filtering bases.double
The fraction of bases that attained at least 60X sequence coverage in post-filtering bases.double
The fraction of bases that attained at least 70X sequence coverage in post-filtering bases.double
The fraction of bases that attained at least 80X sequence coverage in post-filtering bases.double
The fraction of bases that attained at least 90X sequence coverage in post-filtering bases.double
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
The fraction of aligned bases that were filtered out because they were of low base quality (lower than MIN_BASE_QUALITY).double
The fraction of aligned bases that were filtered out because they would have raised coverage above COVERAGE_CAP.double
The fraction of aligned bases that were filtered out because they were in reads marked as duplicates.double
The fraction of aligned bases that were filtered out because they were in reads with low mapping quality (lower than MIN_MAPPING_QUALITY).double
The fraction of aligned bases that were filtered out because they were the second observation from an insert with overlapping reads.double
The total fraction of aligned bases excluded due to all filters.double
The fraction of aligned bases that were filtered out because they were in reads without a mapped mate pair.double
The standard deviation of coverage of the genome after all filters are applied.protected final int
The sample size used for theoretical het sensitivity.protected final htsjdk.samtools.util.Histogram
<Integer> The count of bases observed with a given base quality.protected final htsjdk.samtools.util.Histogram
<Integer> Count of sites with a given depth of coverage. -
Constructor Summary
ConstructorsConstructorDescriptionCreate an instance of this metric that is not mergeable.WgsMetrics
(htsjdk.samtools.util.IntervalList intervals, htsjdk.samtools.util.Histogram<Integer> highQualityDepthHistogram, htsjdk.samtools.util.Histogram<Integer> unfilteredDepthHistogram, double pctExcludedByAdapter, double pctExcludedByMapq, double pctExcludedByDupes, double pctExcludedByPairing, double pctExcludedByBaseq, double pctExcludedByOverlap, double pctExcludedByCapping, double pctExcludeTotal, int coverageCap, htsjdk.samtools.util.Histogram<Integer> unfilteredBaseQHistogram, int theoreticalHetSensitivitySampleSize) Create an instance of this metric that is mergeable. -
Method Summary
Modifier and TypeMethodDescriptionvoid
Placeholder method that will calculate the derived fields from the other ones.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
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Field Details
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intervals
protected htsjdk.samtools.util.IntervalList intervalsThe intervals over which this metric was computed. -
highQualityDepthHistogram
Count of sites with a given depth of coverage. Excludes bases with quality below MINIMUM_BASE_QUALITY -
unfilteredDepthHistogram
Count of sites with a given depth of coverage. Includes all but quality 2 bases -
unfilteredBaseQHistogram
The count of bases observed with a given base quality. -
coverageCap
protected final int coverageCapThe maximum depth/coverage to consider. -
theoreticalHetSensitivitySampleSize
protected final int theoreticalHetSensitivitySampleSizeThe sample size used for theoretical het sensitivity. -
GENOME_TERRITORY
public long GENOME_TERRITORYThe number of non-N bases in the genome reference over which coverage will be evaluated. -
MEAN_COVERAGE
public double MEAN_COVERAGEThe mean coverage in bases of the genome territory, after all filters are applied. -
SD_COVERAGE
public double SD_COVERAGEThe standard deviation of coverage of the genome after all filters are applied. -
MEDIAN_COVERAGE
public double MEDIAN_COVERAGEThe median coverage in bases of the genome territory, after all filters are applied. -
MAD_COVERAGE
public double MAD_COVERAGEThe median absolute deviation of coverage of the genome after all filters are applied. -
PCT_EXC_ADAPTER
public double PCT_EXC_ADAPTERThe 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_MAPQThe 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_DUPEThe fraction of aligned bases that were filtered out because they were in reads marked as duplicates. -
PCT_EXC_UNPAIRED
public double PCT_EXC_UNPAIREDThe 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_BASEQThe 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_OVERLAPThe 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_CAPPEDThe fraction of aligned bases that were filtered out because they would have raised coverage above COVERAGE_CAP. -
PCT_EXC_TOTAL
public double PCT_EXC_TOTALThe total fraction of aligned bases excluded due to all filters. -
PCT_1X
public double PCT_1XThe fraction of bases that attained at least 1X sequence coverage in post-filtering bases. -
PCT_5X
public double PCT_5XThe fraction of bases that attained at least 5X sequence coverage in post-filtering bases. -
PCT_10X
public double PCT_10XThe fraction of bases that attained at least 10X sequence coverage in post-filtering bases. -
PCT_15X
public double PCT_15XThe fraction of bases that attained at least 15X sequence coverage in post-filtering bases. -
PCT_20X
public double PCT_20XThe fraction of bases that attained at least 20X sequence coverage in post-filtering bases. -
PCT_25X
public double PCT_25XThe fraction of bases that attained at least 25X sequence coverage in post-filtering bases. -
PCT_30X
public double PCT_30XThe fraction of bases that attained at least 30X sequence coverage in post-filtering bases. -
PCT_40X
public double PCT_40XThe fraction of bases that attained at least 40X sequence coverage in post-filtering bases. -
PCT_50X
public double PCT_50XThe fraction of bases that attained at least 50X sequence coverage in post-filtering bases. -
PCT_60X
public double PCT_60XThe fraction of bases that attained at least 60X sequence coverage in post-filtering bases. -
PCT_70X
public double PCT_70XThe fraction of bases that attained at least 70X sequence coverage in post-filtering bases. -
PCT_80X
public double PCT_80XThe fraction of bases that attained at least 80X sequence coverage in post-filtering bases. -
PCT_90X
public double PCT_90XThe fraction of bases that attained at least 90X sequence coverage in post-filtering bases. -
PCT_100X
public double PCT_100XThe fraction of bases that attained at least 100X sequence coverage in post-filtering bases. -
FOLD_80_BASE_PENALTY
public double FOLD_80_BASE_PENALTYThe fold over-coverage necessary to raise 80% of bases to the mean coverage level. -
FOLD_90_BASE_PENALTY
public double FOLD_90_BASE_PENALTYThe fold over-coverage necessary to raise 90% of bases to the mean coverage level. -
FOLD_95_BASE_PENALTY
public double FOLD_95_BASE_PENALTYThe fold over-coverage necessary to raise 95% of bases to the mean coverage level. -
HET_SNP_SENSITIVITY
public double HET_SNP_SENSITIVITYThe theoretical HET SNP sensitivity. -
HET_SNP_Q
public double HET_SNP_QThe Phred Scaled Q Score of the theoretical HET SNP sensitivity.
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Constructor Details
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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<Integer> highQualityDepthHistogram, htsjdk.samtools.util.Histogram<Integer> unfilteredDepthHistogram, double pctExcludedByAdapter, double pctExcludedByMapq, double pctExcludedByDupes, double pctExcludedByPairing, double pctExcludedByBaseq, double pctExcludedByOverlap, double pctExcludedByCapping, double pctExcludeTotal, int coverageCap, htsjdk.samtools.util.Histogram<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.
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Method Details
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merge
Merges the various PCT_EXC_* metrics.- Overrides:
merge
in classMergeableMetricBase
- Parameters:
other
- metric to merge into this one.- Returns:
- result of merging, also known as "this"
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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 withNoMergingKeepsValue
.- Overrides:
calculateDerivedFields
in classMergeableMetricBase
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