Package picard.vcf
Class GenotypeConcordanceSummaryMetrics
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- htsjdk.samtools.metrics.MetricBase
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- picard.vcf.GenotypeConcordanceSummaryMetrics
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public class GenotypeConcordanceSummaryMetrics extends htsjdk.samtools.metrics.MetricBase
Class that holds summary metrics about Genotype Concordance
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Field Summary
Fields Modifier and Type Field Description String
CALL_SAMPLE
The name of the 'call' sampledouble
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 calculateddouble
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' sampledouble
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.
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Constructor Summary
Constructors Constructor Description GenotypeConcordanceSummaryMetrics()
Empty constructor - needed for unit testsGenotypeConcordanceSummaryMetrics(htsjdk.variant.variantcontext.VariantContext.Type variantType, GenotypeConcordanceCounts concordanceCounts, String truthSample, String callSample, boolean missingSitesFlag)
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Field Detail
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VARIANT_TYPE
public htsjdk.variant.variantcontext.VariantContext.Type VARIANT_TYPE
The type of the event (i.e. either SNP or INDEL)
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TRUTH_SAMPLE
public String TRUTH_SAMPLE
The name of the 'truth' sample
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CALL_SAMPLE
public String CALL_SAMPLE
The name of the 'call' sample
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HET_SENSITIVITY
public double HET_SENSITIVITY
The sensitivity for all heterozygous variants (Sensitivity is TP / (TP + FN))
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HET_PPV
public double HET_PPV
The ppv (positive predictive value) for all heterozygous variants (PPV is the TP / (TP + FP))
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HET_SPECIFICITY
public double HET_SPECIFICITY
The specificity for all heterozygous variants cannot be calculated
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HOMVAR_SENSITIVITY
public double HOMVAR_SENSITIVITY
The sensitivity for all homozygous variants (Sensitivity is TP / (TP + FN))
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HOMVAR_PPV
public double HOMVAR_PPV
The ppv (positive predictive value) for all homozygous variants (PPV is the TP / (TP + FP))
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HOMVAR_SPECIFICITY
public double HOMVAR_SPECIFICITY
The specificity for all homozygous variants cannot be calculated.
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VAR_SENSITIVITY
public double VAR_SENSITIVITY
The sensitivity for all (heterozygous and homozygous) variants (Sensitivity is TP / (TP + FN))
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VAR_PPV
public double VAR_PPV
The ppv (positive predictive value) for all (heterozygous and homozygous) variants (PPV is the TP / (TP + FP))
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VAR_SPECIFICITY
public double VAR_SPECIFICITY
The specificity for all (heterozygous and homozygous) variants (Specificity is TN / (FP + TN))
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GENOTYPE_CONCORDANCE
public double GENOTYPE_CONCORDANCE
The 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
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NON_REF_GENOTYPE_CONCORDANCE
public double NON_REF_GENOTYPE_CONCORDANCE
The 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 Detail
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GenotypeConcordanceSummaryMetrics
public GenotypeConcordanceSummaryMetrics()
Empty constructor - needed for unit tests
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GenotypeConcordanceSummaryMetrics
public GenotypeConcordanceSummaryMetrics(htsjdk.variant.variantcontext.VariantContext.Type variantType, GenotypeConcordanceCounts concordanceCounts, String truthSample, String callSample, boolean missingSitesFlag)
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