public class GenotypeConcordanceSummaryMetrics
extends htsjdk.samtools.metrics.MetricBase
Modifier and Type | Field | Description |
---|---|---|
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.
|
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 | Description |
---|---|
GenotypeConcordanceSummaryMetrics() |
Empty constructor - needed for unit tests
|
GenotypeConcordanceSummaryMetrics(htsjdk.variant.variantcontext.VariantContext.Type variantType,
GenotypeConcordanceCounts concordanceCounts,
String truthSample,
String callSample,
boolean missingSitesFlag) |
public htsjdk.variant.variantcontext.VariantContext.Type VARIANT_TYPE
public String TRUTH_SAMPLE
public 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, String truthSample, String callSample, boolean missingSitesFlag)