Package picard.vcf

Class GenotypeConcordanceDetailMetrics


  • public class GenotypeConcordanceDetailMetrics
    extends htsjdk.samtools.metrics.MetricBase
    Class that holds detail metrics about Genotype Concordance
    • 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
      • COUNT

        public long COUNT
        The number of events of type TRUTH_STATE and CALL_STATE for the EVENT_TYPE and SAMPLEs
      • CONTINGENCY_VALUES

        public String CONTINGENCY_VALUES
        The list of contingency table values (TP, TN, FP, FN) that are deduced from the truth/call state comparison, given the reference. In general, we are comparing two sets of alleles. Therefore, we can have zero or more contingency table values represented in one comparison. For example, if the truthset is a heterozygous call with both alleles non-reference (HET_VAR1_VAR2), and the callset is a heterozygous call with both alleles non-reference with one of the alternate alleles matching an alternate allele in the callset, we would have a true positive, false positive, and false negative. The true positive is from the matching alternate alleles, the false positive is the alternate allele found in the callset but not found in the truthset, and the false negative is the alternate in the truthset not found in the callset. We also include a true negative in cases where the reference allele is found in both the truthset and callset.
    • Constructor Detail

      • GenotypeConcordanceDetailMetrics

        public GenotypeConcordanceDetailMetrics()