Package picard.vcf
Class CollectVariantCallingMetrics.VariantCallingDetailMetrics
java.lang.Object
htsjdk.samtools.metrics.MetricBase
picard.analysis.MergeableMetricBase
picard.vcf.CollectVariantCallingMetrics.VariantCallingSummaryMetrics
picard.vcf.CollectVariantCallingMetrics.VariantCallingDetailMetrics
- Enclosing class:
- CollectVariantCallingMetrics
@DocumentedFeature(groupName="Metrics",
summary="Metrics")
public static class CollectVariantCallingMetrics.VariantCallingDetailMetrics
extends CollectVariantCallingMetrics.VariantCallingSummaryMetrics
A collection of metrics relating to snps and indels within a variant-calling file (VCF) for a given sample.
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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 TypeFieldDescriptiondouble
(count of hets)/(count of homozygous non-ref) for this sampledouble
The percentage of variants in a particular sample that have a GQ score of 0.The name of the sample being assayedlong
The total number of variants in a particular sample that have a GQ score of 0.long
total number of reads (from AD field) for passing bi-allelic SNP hets for this sampleFields inherited from class picard.vcf.CollectVariantCallingMetrics.VariantCallingSummaryMetrics
DBSNP_INS_DEL_RATIO, DBSNP_TITV, FILTERED_INDELS, FILTERED_SNPS, NOVEL_INDELS, NOVEL_INS_DEL_RATIO, NOVEL_SNPS, NOVEL_TITV, NUM_IN_DB_SNP, NUM_IN_DB_SNP_COMPLEX_INDELS, NUM_IN_DB_SNP_INDELS, NUM_IN_DB_SNP_MULTIALLELIC, NUM_SINGLETONS, PCT_DBSNP, PCT_DBSNP_INDELS, SNP_REFERENCE_BIAS, TOTAL_COMPLEX_INDELS, TOTAL_INDELS, TOTAL_MULTIALLELIC_SNPS, TOTAL_SNPS
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Constructor Summary
Constructors -
Method Summary
Modifier and TypeMethodDescriptionvoid
Placeholder method that will calculate the derived fields from the other ones.void
static String
Methods inherited from class picard.vcf.CollectVariantCallingMetrics.VariantCallingSummaryMetrics
calculateFromDerivedFields, 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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SAMPLE_ALIAS
The name of the sample being assayed -
HET_HOMVAR_RATIO
public double HET_HOMVAR_RATIO(count of hets)/(count of homozygous non-ref) for this sample -
PCT_GQ0_VARIANTS
public double PCT_GQ0_VARIANTSThe percentage of variants in a particular sample that have a GQ score of 0. -
TOTAL_GQ0_VARIANTS
public long TOTAL_GQ0_VARIANTSThe total number of variants in a particular sample that have a GQ score of 0. -
TOTAL_HET_DEPTH
public long TOTAL_HET_DEPTHtotal number of reads (from AD field) for passing bi-allelic SNP hets for this sample
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Constructor Details
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VariantCallingDetailMetrics
public VariantCallingDetailMetrics()
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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 classCollectVariantCallingMetrics.VariantCallingSummaryMetrics
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calculateFromDerivedFields
public void calculateFromDerivedFields()
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