Class FingerprintingSummaryMetrics


  • @DocumentedFeature(groupName="Metrics",
                       summary="Metrics")
    public class FingerprintingSummaryMetrics
    extends htsjdk.samtools.metrics.MetricBase
    Summary fingerprinting metrics and statistics about the comparison of the sequence data from a single read group (lane or index within a lane) vs. a set of known genotypes for the expected sample.
    • Field Detail

      • READ_GROUP

        public String READ_GROUP
        The read group from which sequence data was drawn for comparison.
      • SAMPLE

        public String SAMPLE
        The sample whose known genotypes the sequence data was compared to.
      • LL_EXPECTED_SAMPLE

        public double LL_EXPECTED_SAMPLE
        The Log Likelihood of the sequence data given the expected sample's genotypes.
      • LL_RANDOM_SAMPLE

        public double LL_RANDOM_SAMPLE
        The Log Likelihood of the sequence data given a random sample from the human population.
      • LOD_EXPECTED_SAMPLE

        public double LOD_EXPECTED_SAMPLE
        The LOD for Expected Sample vs. Random Sample. A positive LOD indicates that the sequence data is more likely to come from the expected sample vs. a random sample from the population, by LOD logs. I.e. a value of 6 indicates that the sequence data is 1,000,000 more likely to come from the expected sample than from a random sample. A negative LOD indicates the reverse - that the sequence data is more likely to come from a random sample than from the expected sample.
      • HAPLOTYPES_WITH_GENOTYPES

        public int HAPLOTYPES_WITH_GENOTYPES
        The number of haplotypes that had expected genotypes to compare to.
      • HAPLOTYPES_CONFIDENTLY_CHECKED

        public int HAPLOTYPES_CONFIDENTLY_CHECKED
        The subset of genotyped haplotypes for which there was sufficient sequence data to confidently genotype the haplotype. Note: all haplotypes with sequence coverage contribute to the LOD score, even if they cannot be "confidently checked" individually.
      • HAPLOTYPES_CONFIDENTLY_MATCHING

        public int HAPLOTYPES_CONFIDENTLY_MATCHING
        The subset of confidently checked haplotypes that match the expected genotypes.
      • HET_AS_HOM

        public int HET_AS_HOM
        num of hets, observed as homs with LOD > threshold
      • HOM_AS_HET

        public int HOM_AS_HET
        num of homs, observed as hets with LOD > threshold
      • HOM_AS_OTHER_HOM

        public int HOM_AS_OTHER_HOM
        num of homs, observed as other homs with LOD > threshold
    • Constructor Detail

      • FingerprintingSummaryMetrics

        public FingerprintingSummaryMetrics()