Package picard.arrays
Class CollectArraysVariantCallingMetrics.ArraysVariantCallingDetailMetrics
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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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- picard.arrays.CollectArraysVariantCallingMetrics.ArraysVariantCallingDetailMetrics
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- Enclosing class:
- CollectArraysVariantCallingMetrics
public static class CollectArraysVariantCallingMetrics.ArraysVariantCallingDetailMetrics extends CollectArraysVariantCallingMetrics.ArraysVariantCallingSummaryMetrics
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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 Integer
ANALYSIS_VERSION
The version number of the analysis runhtsjdk.samtools.util.Iso8601Date
AUTOCALL_DATE
The date this sample was autocalledString
AUTOCALL_GENDER
The sex, as determined by AutocallBoolean
AUTOCALL_PF
Whether the sample passes QC based on call rate thresholdString
AUTOCALL_VERSION
The version of autocall used for calling this sampleString
CHIP_TYPE
The chip type nameString
CHIP_WELL_BARCODE
The chip well barcode of the Illumina array being assayedString
CLUSTER_FILE_NAME
The name of the cluster file usedString
EXTENDED_MANIFEST_VERSION
The version of the Extended Illumina Manifest used for calling this sampleString
FP_GENDER
The sex, as reported for the fingerprinted sampleBoolean
GENDER_CONCORDANCE_PF
Whether or not the three sexs agreedouble
HET_HOMVAR_RATIO
(count of hets)/(count of homozygous non-ref) for this sampledouble
HET_PCT
100 * (count of hets) / (total calls) for this samplehtsjdk.samtools.util.Iso8601Date
IMAGING_DATE
The date that this sample was imagedBoolean
IS_ZCALLED
Whether the sample was zcalledInteger
P95_GREEN
The 95th Intensity Percentile for the green color channel for this sampleInteger
P95_RED
The 95th Intensity Percentile for the red color channel for this sampleString
REPORTED_GENDER
The sex, as reported by the collaboratorString
SAMPLE_ALIAS
The name of the sampleString
SCANNER_NAME
The name of the scanner used for this sampleString
ZCALL_VERSION
The version of ZCall used for calling this sample-
Fields 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 Constructor Description ArraysVariantCallingDetailMetrics()
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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 String
getFileExtension()
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Methods inherited from class picard.arrays.CollectArraysVariantCallingMetrics.ArraysVariantCallingSummaryMetrics
foldInto
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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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CHIP_WELL_BARCODE
public String CHIP_WELL_BARCODE
The chip well barcode of the Illumina array being assayed
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SAMPLE_ALIAS
public String SAMPLE_ALIAS
The name of the sample
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ANALYSIS_VERSION
public Integer ANALYSIS_VERSION
The version number of the analysis run
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CHIP_TYPE
public String CHIP_TYPE
The chip type name
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AUTOCALL_PF
public Boolean AUTOCALL_PF
Whether the sample passes QC based on call rate threshold
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AUTOCALL_DATE
public htsjdk.samtools.util.Iso8601Date AUTOCALL_DATE
The date this sample was autocalled
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IMAGING_DATE
public htsjdk.samtools.util.Iso8601Date IMAGING_DATE
The date that this sample was imaged
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IS_ZCALLED
public Boolean IS_ZCALLED
Whether the sample was zcalled
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AUTOCALL_GENDER
public String AUTOCALL_GENDER
The sex, as determined by Autocall
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FP_GENDER
public String FP_GENDER
The sex, as reported for the fingerprinted sample
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REPORTED_GENDER
public String REPORTED_GENDER
The sex, as reported by the collaborator
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GENDER_CONCORDANCE_PF
public Boolean GENDER_CONCORDANCE_PF
Whether or not the three sexs agree
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HET_PCT
public double HET_PCT
100 * (count of hets) / (total calls) for this sample
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CLUSTER_FILE_NAME
public String CLUSTER_FILE_NAME
The name of the cluster file used
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P95_GREEN
public Integer P95_GREEN
The 95th Intensity Percentile for the green color channel for this sample
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P95_RED
public Integer P95_RED
The 95th Intensity Percentile for the red color channel for this sample
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AUTOCALL_VERSION
public String AUTOCALL_VERSION
The version of autocall used for calling this sample
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ZCALL_VERSION
public String ZCALL_VERSION
The version of ZCall used for calling this sample
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EXTENDED_MANIFEST_VERSION
public String EXTENDED_MANIFEST_VERSION
The version of the Extended Illumina Manifest used for calling this sample
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HET_HOMVAR_RATIO
public double HET_HOMVAR_RATIO
(count of hets)/(count of homozygous non-ref) for this sample
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SCANNER_NAME
public String SCANNER_NAME
The name of the scanner used for this sample
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Method Detail
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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
public static String getFileExtension()
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