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
  • Field Summary

    Fields
    Modifier and Type
    Field
    Description
    The name of the 'call' sample
    double
    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 calculated
    double
    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' sample
    double
    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

    Constructors
    Constructor
    Description
    Empty constructor - needed for unit tests
    GenotypeConcordanceSummaryMetrics(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

    Methods inherited from class java.lang.Object

    clone, finalize, getClass, notify, notifyAll, wait, wait, wait
  • Field Details

    • 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 Details

    • 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)