Package picard.arrays
Class CollectArraysVariantCallingMetrics.ArraysVariantCallingSummaryMetrics
java.lang.Object
htsjdk.samtools.metrics.MetricBase
picard.analysis.MergeableMetricBase
picard.arrays.CollectArraysVariantCallingMetrics.ArraysVariantCallingSummaryMetrics
- Direct Known Subclasses:
CollectArraysVariantCallingMetrics.ArraysVariantCallingDetailMetrics
- Enclosing class:
CollectArraysVariantCallingMetrics
@DocumentedFeature(groupName="Metrics",
summary="Metrics")
public static class CollectArraysVariantCallingMetrics.ArraysVariantCallingSummaryMetrics
extends MergeableMetricBase
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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 TypeFieldDescriptionfloat
The overall autocall call ratefloat
The overall call ratelong
The number of high confidence SNPS called that were not found in dbSNPlong
The total number of assays (SNP and indels) in the VCFlong
The number of passing autocall callslong
The number of passing callslong
The total number of filtered assays in the VCFlong
The number of high confidence SNPs found in dbSNPlong
The number of indel callslong
The number of no-callslong
The total number of NON-filtered assays in the VCFlong
For summary metrics, the number of variants that appear in only one sample.long
The number of bi-allelic SNP callslong
The total number of zeroed-out (filtered out by Illumina in chip design) assays in the VCFfloat
The fraction of high confidence SNPs in dbSNP -
Constructor Summary
Constructors -
Method Summary
Modifier and TypeMethodDescriptionvoid
Placeholder method that will calculate the derived fields from the other ones.static <T extends CollectArraysVariantCallingMetrics.ArraysVariantCallingSummaryMetrics>
voidfoldInto
(CollectArraysVariantCallingMetrics.ArraysVariantCallingSummaryMetrics target, Collection<CollectArraysVariantCallingMetrics.ArraysVariantCallingDetailMetrics> metrics) static String
Methods inherited from class picard.analysis.MergeableMetricBase
canMerge, merge, merge, mergeIfCan
Methods inherited from class htsjdk.samtools.metrics.MetricBase
equals, hashCode, toString
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Field Details
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NUM_ASSAYS
public long NUM_ASSAYSThe total number of assays (SNP and indels) in the VCF -
NUM_NON_FILTERED_ASSAYS
public long NUM_NON_FILTERED_ASSAYSThe total number of NON-filtered assays in the VCF -
NUM_FILTERED_ASSAYS
public long NUM_FILTERED_ASSAYSThe total number of filtered assays in the VCF -
NUM_ZEROED_OUT_ASSAYS
public long NUM_ZEROED_OUT_ASSAYSThe total number of zeroed-out (filtered out by Illumina in chip design) assays in the VCF -
NUM_SNPS
public long NUM_SNPSThe number of bi-allelic SNP calls -
NUM_INDELS
public long NUM_INDELSThe number of indel calls -
NUM_CALLS
public long NUM_CALLSThe number of passing calls -
NUM_AUTOCALL_CALLS
public long NUM_AUTOCALL_CALLSThe number of passing autocall calls -
NUM_NO_CALLS
public long NUM_NO_CALLSThe number of no-calls -
NUM_IN_DB_SNP
public long NUM_IN_DB_SNPThe number of high confidence SNPs found in dbSNP -
NOVEL_SNPS
public long NOVEL_SNPSThe number of high confidence SNPS called that were not found in dbSNP -
PCT_DBSNP
public float PCT_DBSNPThe fraction of high confidence SNPs in dbSNP -
CALL_RATE
public float CALL_RATEThe overall call rate -
AUTOCALL_CALL_RATE
public float AUTOCALL_CALL_RATEThe overall autocall call rate -
NUM_SINGLETONS
public long NUM_SINGLETONSFor summary metrics, the number of variants that appear in only one sample. For detail metrics, the number of variants that appear only in the current sample.
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Constructor Details
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ArraysVariantCallingSummaryMetrics
public ArraysVariantCallingSummaryMetrics()
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Method Details
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getFileExtension
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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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foldInto
public static <T extends CollectArraysVariantCallingMetrics.ArraysVariantCallingSummaryMetrics> void foldInto(CollectArraysVariantCallingMetrics.ArraysVariantCallingSummaryMetrics target, Collection<CollectArraysVariantCallingMetrics.ArraysVariantCallingDetailMetrics> metrics)
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