Package picard.arrays
Class CollectArraysVariantCallingMetrics.ArraysVariantCallingDetailMetrics
java.lang.Object
htsjdk.samtools.metrics.MetricBase
picard.analysis.MergeableMetricBase
picard.arrays.CollectArraysVariantCallingMetrics.ArraysVariantCallingSummaryMetrics
picard.arrays.CollectArraysVariantCallingMetrics.ArraysVariantCallingDetailMetrics
- Enclosing class:
- CollectArraysVariantCallingMetrics
@DocumentedFeature(groupName="Metrics",
summary="Metrics")
public static class CollectArraysVariantCallingMetrics.ArraysVariantCallingDetailMetrics
extends CollectArraysVariantCallingMetrics.ArraysVariantCallingSummaryMetrics
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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 TypeFieldDescriptionThe version number of the analysis runhtsjdk.samtools.util.Iso8601Date
The date this sample was autocalledThe sex, as determined by AutocallWhether the sample passes QC based on call rate thresholdThe version of autocall used for calling this sampleThe chip type nameThe chip well barcode of the Illumina array being assayedThe name of the cluster file usedThe version of the Extended Illumina Manifest used for calling this sampleThe sex, as reported for the fingerprinted sampleWhether or not the three sexs agreeThe call rate as determined by Autocall/IAAP (and stored in the GTC File)double
(count of hets)/(count of homozygous non-ref) for this sampledouble
100 * (count of hets) / (total calls) for this samplehtsjdk.samtools.util.Iso8601Date
The date that this sample was imagedWhether the sample was zcalledThe 95th Intensity Percentile for the green color channel for this sampleThe 95th Intensity Percentile for the red color channel for this sampleThe version of the pipeline used for this sampleThe sex, as reported by the collaboratorThe name of the sampleThe name of the scanner used for this sampleThe version of ZCall used for calling this sampleFields inherited from class picard.arrays.CollectArraysVariantCallingMetrics.ArraysVariantCallingSummaryMetrics
AUTOCALL_CALL_RATE, CALL_RATE, NOVEL_SNPS, NUM_ASSAYS, NUM_AUTOCALL_CALLS, NUM_CALLS, NUM_FILTERED_ASSAYS, NUM_IN_DB_SNP, NUM_INDELS, NUM_NO_CALLS, NUM_NON_FILTERED_ASSAYS, NUM_SINGLETONS, NUM_SNPS, NUM_ZEROED_OUT_ASSAYS, PCT_DBSNP
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Constructor Summary
Constructors -
Method Summary
Modifier and TypeMethodDescriptionvoid
Placeholder method that will calculate the derived fields from the other ones.static String
Methods inherited from class picard.arrays.CollectArraysVariantCallingMetrics.ArraysVariantCallingSummaryMetrics
foldInto
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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CHIP_WELL_BARCODE
The chip well barcode of the Illumina array being assayed -
SAMPLE_ALIAS
The name of the sample -
ANALYSIS_VERSION
The version number of the analysis run -
CHIP_TYPE
The chip type name -
AUTOCALL_PF
Whether the sample passes QC based on call rate threshold -
AUTOCALL_DATE
public htsjdk.samtools.util.Iso8601Date AUTOCALL_DATEThe date this sample was autocalled -
IMAGING_DATE
public htsjdk.samtools.util.Iso8601Date IMAGING_DATEThe date that this sample was imaged -
IS_ZCALLED
Whether the sample was zcalled -
GTC_CALL_RATE
The call rate as determined by Autocall/IAAP (and stored in the GTC File) -
AUTOCALL_GENDER
The sex, as determined by Autocall -
FP_GENDER
The sex, as reported for the fingerprinted sample -
REPORTED_GENDER
The sex, as reported by the collaborator -
GENDER_CONCORDANCE_PF
Whether or not the three sexs agree -
HET_PCT
public double HET_PCT100 * (count of hets) / (total calls) for this sample -
CLUSTER_FILE_NAME
The name of the cluster file used -
P95_GREEN
The 95th Intensity Percentile for the green color channel for this sample -
P95_RED
The 95th Intensity Percentile for the red color channel for this sample -
AUTOCALL_VERSION
The version of autocall used for calling this sample -
ZCALL_VERSION
The version of ZCall used for calling this sample -
EXTENDED_MANIFEST_VERSION
The version of the Extended Illumina Manifest used for calling this sample -
HET_HOMVAR_RATIO
public double HET_HOMVAR_RATIO(count of hets)/(count of homozygous non-ref) for this sample -
SCANNER_NAME
The name of the scanner used for this sample -
PIPELINE_VERSION
The version of the pipeline used for this sample
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Constructor Details
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ArraysVariantCallingDetailMetrics
public ArraysVariantCallingDetailMetrics()
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Method Details
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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
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getFileExtension
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