Package picard.arrays
Class CollectArraysVariantCallingMetrics.ArraysVariantCallingSummaryMetrics
- java.lang.Object
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- htsjdk.samtools.metrics.MetricBase
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- picard.analysis.MergeableMetricBase
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- picard.arrays.CollectArraysVariantCallingMetrics.ArraysVariantCallingSummaryMetrics
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- Direct Known Subclasses:
CollectArraysVariantCallingMetrics.ArraysVariantCallingDetailMetrics
- Enclosing class:
- CollectArraysVariantCallingMetrics
public static class CollectArraysVariantCallingMetrics.ArraysVariantCallingSummaryMetrics extends MergeableMetricBase
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Nested Class Summary
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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
Fields Modifier and Type Field Description float
AUTOCALL_CALL_RATE
The overall autocall call ratefloat
CALL_RATE
The overall call ratelong
NOVEL_SNPS
The number of high confidence SNPS called that were not found in dbSNPlong
NUM_ASSAYS
The total number of assays (SNP and indels) in the VCFlong
NUM_AUTOCALL_CALLS
The number of passing autocall callslong
NUM_CALLS
The number of passing callslong
NUM_FILTERED_ASSAYS
The total number of filtered assays in the VCFlong
NUM_IN_DB_SNP
The number of high confidence SNPs found in dbSNPlong
NUM_INDELS
The number of indel callslong
NUM_NO_CALLS
The number of no-callslong
NUM_NON_FILTERED_ASSAYS
The total number of NON-filtered assays in the VCFlong
NUM_SINGLETONS
For summary metrics, the number of variants that appear in only one sample.long
NUM_SNPS
The number of bi-allelic SNP callslong
NUM_ZEROED_OUT_ASSAYS
The total number of zeroed-out (filtered out by Illumina in chip design) assays in the VCFfloat
PCT_DBSNP
The fraction of high confidence SNPs in dbSNP
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Constructor Summary
Constructors Constructor Description ArraysVariantCallingSummaryMetrics()
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Method Summary
All Methods Static Methods Instance Methods Concrete Methods Modifier and Type Method Description void
calculateDerivedFields()
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
getFileExtension()
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Methods inherited from class picard.analysis.MergeableMetricBase
canMerge, merge, merge, mergeIfCan
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Field Detail
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NUM_ASSAYS
public long NUM_ASSAYS
The total number of assays (SNP and indels) in the VCF
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NUM_NON_FILTERED_ASSAYS
public long NUM_NON_FILTERED_ASSAYS
The total number of NON-filtered assays in the VCF
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NUM_FILTERED_ASSAYS
public long NUM_FILTERED_ASSAYS
The total number of filtered assays in the VCF
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NUM_ZEROED_OUT_ASSAYS
public long NUM_ZEROED_OUT_ASSAYS
The total number of zeroed-out (filtered out by Illumina in chip design) assays in the VCF
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NUM_SNPS
public long NUM_SNPS
The number of bi-allelic SNP calls
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NUM_INDELS
public long NUM_INDELS
The number of indel calls
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NUM_CALLS
public long NUM_CALLS
The number of passing calls
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NUM_AUTOCALL_CALLS
public long NUM_AUTOCALL_CALLS
The number of passing autocall calls
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NUM_NO_CALLS
public long NUM_NO_CALLS
The number of no-calls
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NUM_IN_DB_SNP
public long NUM_IN_DB_SNP
The number of high confidence SNPs found in dbSNP
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NOVEL_SNPS
public long NOVEL_SNPS
The number of high confidence SNPS called that were not found in dbSNP
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PCT_DBSNP
public float PCT_DBSNP
The fraction of high confidence SNPs in dbSNP
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CALL_RATE
public float CALL_RATE
The overall call rate
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AUTOCALL_CALL_RATE
public float AUTOCALL_CALL_RATE
The overall autocall call rate
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NUM_SINGLETONS
public long NUM_SINGLETONS
For 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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Method Detail
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getFileExtension
public static String 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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