Package picard.vcf
Class GenotypeConcordanceSummaryMetrics
java.lang.Object
htsjdk.samtools.metrics.MetricBase
picard.vcf.GenotypeConcordanceSummaryMetrics
@DocumentedFeature(groupName="Metrics",
summary="Metrics")
public class GenotypeConcordanceSummaryMetrics
extends htsjdk.samtools.metrics.MetricBase
Class that holds summary metrics about Genotype Concordance
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Field Summary
FieldsModifier and TypeFieldDescriptionThe name of the 'call' sampledouble
The genotype concordance for all possible states.double
The ppv (positive predictive value) for all heterozygous variants (PPV is the TP / (TP + FP))double
The sensitivity for all heterozygous variants (Sensitivity is TP / (TP + FN))double
The specificity for all heterozygous variants cannot be calculateddouble
The ppv (positive predictive value) for all homozygous variants (PPV is the TP / (TP + FP))double
The sensitivity for all homozygous variants (Sensitivity is TP / (TP + FN))double
The specificity for all homozygous variants cannot be calculated.double
The non-ref genotype concordance, ie for all var states only.The name of the 'truth' sampledouble
The ppv (positive predictive value) for all (heterozygous and homozygous) variants (PPV is the TP / (TP + FP))double
The sensitivity for all (heterozygous and homozygous) variants (Sensitivity is TP / (TP + FN))double
The specificity for all (heterozygous and homozygous) variants (Specificity is TN / (FP + TN))htsjdk.variant.variantcontext.VariantContext.Type
The type of the event (i.e. -
Constructor Summary
ConstructorsConstructorDescriptionEmpty constructor - needed for unit testsGenotypeConcordanceSummaryMetrics
(htsjdk.variant.variantcontext.VariantContext.Type variantType, GenotypeConcordanceCounts concordanceCounts, String truthSample, String callSample, boolean missingSitesFlag) -
Method Summary
Methods inherited from class htsjdk.samtools.metrics.MetricBase
equals, hashCode, toString
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Field Details
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VARIANT_TYPE
public htsjdk.variant.variantcontext.VariantContext.Type VARIANT_TYPEThe type of the event (i.e. either SNP or INDEL) -
TRUTH_SAMPLE
The name of the 'truth' sample -
CALL_SAMPLE
The name of the 'call' sample -
HET_SENSITIVITY
public double HET_SENSITIVITYThe sensitivity for all heterozygous variants (Sensitivity is TP / (TP + FN)) -
HET_PPV
public double HET_PPVThe ppv (positive predictive value) for all heterozygous variants (PPV is the TP / (TP + FP)) -
HET_SPECIFICITY
public double HET_SPECIFICITYThe specificity for all heterozygous variants cannot be calculated -
HOMVAR_SENSITIVITY
public double HOMVAR_SENSITIVITYThe sensitivity for all homozygous variants (Sensitivity is TP / (TP + FN)) -
HOMVAR_PPV
public double HOMVAR_PPVThe ppv (positive predictive value) for all homozygous variants (PPV is the TP / (TP + FP)) -
HOMVAR_SPECIFICITY
public double HOMVAR_SPECIFICITYThe specificity for all homozygous variants cannot be calculated. -
VAR_SENSITIVITY
public double VAR_SENSITIVITYThe sensitivity for all (heterozygous and homozygous) variants (Sensitivity is TP / (TP + FN)) -
VAR_PPV
public double VAR_PPVThe ppv (positive predictive value) for all (heterozygous and homozygous) variants (PPV is the TP / (TP + FP)) -
VAR_SPECIFICITY
public double VAR_SPECIFICITYThe specificity for all (heterozygous and homozygous) variants (Specificity is TN / (FP + TN)) -
GENOTYPE_CONCORDANCE
public double GENOTYPE_CONCORDANCEThe genotype concordance for all possible states. Genotype Concordance is the number of times the truth and call states match exactly / all truth and call combinations made -
NON_REF_GENOTYPE_CONCORDANCE
public double NON_REF_GENOTYPE_CONCORDANCEThe non-ref genotype concordance, ie for all var states only. Non Ref Genotype Concordance is the number of times the truth and call states match exactly for *vars only* / all truth and call *var* combinations made
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Constructor Details
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GenotypeConcordanceSummaryMetrics
public GenotypeConcordanceSummaryMetrics()Empty constructor - needed for unit tests -
GenotypeConcordanceSummaryMetrics
public GenotypeConcordanceSummaryMetrics(htsjdk.variant.variantcontext.VariantContext.Type variantType, GenotypeConcordanceCounts concordanceCounts, String truthSample, String callSample, boolean missingSitesFlag)
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