public class GenotypeConcordanceSummaryMetrics
extends htsjdk.samtools.metrics.MetricBase
Modifier and Type | Field and Description |
---|---|
java.lang.String |
CALL_SAMPLE
The name of the 'call' sample
|
double |
GENOTYPE_CONCORDANCE
The genotype concordance for all possible states.
|
double |
HET_PPV
The ppv (positive predictive value) for all heterozygous variants (PPV is the TP / (TP + FP))
|
double |
HET_SENSITIVITY
The sensitivity for all heterozygous variants (Sensitivity is TP / (TP + FN))
|
double |
HET_SPECIFICITY
The specificity for all heterozygous variants cannot be calculated
|
double |
HOMVAR_PPV
The ppv (positive predictive value) for all homozygous variants (PPV is the TP / (TP + FP))
|
double |
HOMVAR_SENSITIVITY
The sensitivity for all homozygous variants (Sensitivity is TP / (TP + FN))
|
double |
HOMVAR_SPECIFICITY
The specificity for all homozygous variants cannot be calculated.
|
double |
NON_REF_GENOTYPE_CONCORDANCE
The non-ref genotype concordance, ie for all var states only.
|
java.lang.String |
TRUTH_SAMPLE
The name of the 'truth' sample
|
double |
VAR_PPV
The ppv (positive predictive value) for all (heterozygous and homozygous) variants (PPV is the TP / (TP + FP))
|
double |
VAR_SENSITIVITY
The sensitivity for all (heterozygous and homozygous) variants (Sensitivity is TP / (TP + FN))
|
double |
VAR_SPECIFICITY
The specificity for all (heterozygous and homozygous) variants (Specificity is TN / (FP + TN))
|
htsjdk.variant.variantcontext.VariantContext.Type |
VARIANT_TYPE
The type of the event (i.e.
|
Constructor and Description |
---|
GenotypeConcordanceSummaryMetrics()
Empty constructor - needed for unit tests
|
GenotypeConcordanceSummaryMetrics(htsjdk.variant.variantcontext.VariantContext.Type variantType,
GenotypeConcordanceCounts concordanceCounts,
java.lang.String truthSample,
java.lang.String callSample,
boolean missingSitesFlag) |
public htsjdk.variant.variantcontext.VariantContext.Type VARIANT_TYPE
public java.lang.String TRUTH_SAMPLE
public java.lang.String CALL_SAMPLE
public double HET_SENSITIVITY
public double HET_PPV
public double HET_SPECIFICITY
public double HOMVAR_SENSITIVITY
public double HOMVAR_PPV
public double HOMVAR_SPECIFICITY
public double VAR_SENSITIVITY
public double VAR_PPV
public double VAR_SPECIFICITY
public double GENOTYPE_CONCORDANCE
public double NON_REF_GENOTYPE_CONCORDANCE
public GenotypeConcordanceSummaryMetrics()
public GenotypeConcordanceSummaryMetrics(htsjdk.variant.variantcontext.VariantContext.Type variantType, GenotypeConcordanceCounts concordanceCounts, java.lang.String truthSample, java.lang.String callSample, boolean missingSitesFlag)