Class FingerprintingSummaryMetrics

java.lang.Object
htsjdk.samtools.metrics.MetricBase
picard.analysis.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 Details

    • 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 Details

    • FingerprintingSummaryMetrics

      public FingerprintingSummaryMetrics()