Package picard.vcf

Class GenotypeConcordanceSummaryMetrics


  • @DocumentedFeature(groupName="Metrics",
                       summary="Metrics")
    public class GenotypeConcordanceSummaryMetrics
    extends htsjdk.samtools.metrics.MetricBase
    Class that holds summary metrics about Genotype Concordance
    • Field Summary

      Fields 
      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.
    • Field Detail

      • VARIANT_TYPE

        public htsjdk.variant.variantcontext.VariantContext.Type VARIANT_TYPE
        The type of the event (i.e. either SNP or INDEL)
      • TRUTH_SAMPLE

        public String TRUTH_SAMPLE
        The name of the 'truth' sample
      • CALL_SAMPLE

        public String CALL_SAMPLE
        The name of the 'call' sample
      • HET_SENSITIVITY

        public double HET_SENSITIVITY
        The sensitivity for all heterozygous variants (Sensitivity is TP / (TP + FN))
      • HET_PPV

        public double HET_PPV
        The ppv (positive predictive value) for all heterozygous variants (PPV is the TP / (TP + FP))
      • HET_SPECIFICITY

        public double HET_SPECIFICITY
        The specificity for all heterozygous variants cannot be calculated
      • HOMVAR_SENSITIVITY

        public double HOMVAR_SENSITIVITY
        The sensitivity for all homozygous variants (Sensitivity is TP / (TP + FN))
      • HOMVAR_PPV

        public double HOMVAR_PPV
        The ppv (positive predictive value) for all homozygous variants (PPV is the TP / (TP + FP))
      • HOMVAR_SPECIFICITY

        public double HOMVAR_SPECIFICITY
        The specificity for all homozygous variants cannot be calculated.
      • VAR_SENSITIVITY

        public double VAR_SENSITIVITY
        The sensitivity for all (heterozygous and homozygous) variants (Sensitivity is TP / (TP + FN))
      • VAR_PPV

        public double VAR_PPV
        The ppv (positive predictive value) for all (heterozygous and homozygous) variants (PPV is the TP / (TP + FP))
      • VAR_SPECIFICITY

        public double VAR_SPECIFICITY
        The specificity for all (heterozygous and homozygous) variants (Specificity is TN / (FP + TN))
      • 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
      • 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
    • Constructor Detail

      • 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)