Class IndependentReplicateMetric

java.lang.Object
htsjdk.samtools.metrics.MetricBase
picard.analysis.MergeableMetricBase
picard.analysis.replicates.IndependentReplicateMetric

@DocumentedFeature(groupName="Metrics", summary="Metrics") public class IndependentReplicateMetric extends MergeableMetricBase
A class to store information relevant for biological rate estimation
  • Field Details

    • nSites

      public Integer nSites
      The count of sites used.
    • nThreeAllelesSites

      public Integer nThreeAllelesSites
      The count of sites in which a third allele was found.
    • nTotalReads

      public Integer nTotalReads
      The total number of reads over the het sites.
    • nDuplicateSets

      public Integer nDuplicateSets
      The number of duplicate sets examined.
    • nExactlyTriple

      public Integer nExactlyTriple
      The number of sets of size exactly 3 found.
    • nExactlyDouble

      public Integer nExactlyDouble
      The number of sets of size exactly 2 found.
    • nReadsInBigSets

      public Integer nReadsInBigSets
      The number of reads in duplicate of sizes greater than 3.
    • nDifferentAllelesBiDups

      public Integer nDifferentAllelesBiDups
      The number of doubletons where the two reads had different bases in the locus.
    • nReferenceAllelesBiDups

      public Integer nReferenceAllelesBiDups
      The number of doubletons where the two reads matched the reference.
    • nAlternateAllelesBiDups

      public Integer nAlternateAllelesBiDups
      The number of doubletons where the two reads matched the alternate.
    • nDifferentAllelesTriDups

      public Integer nDifferentAllelesTriDups
      The number of tripletons where at least one of the reads didn't match either allele of the het site.
    • nMismatchingAllelesBiDups

      public Integer nMismatchingAllelesBiDups
      The number of tripletons where the two reads had different bases in the locus.
    • nReferenceAllelesTriDups

      public Integer nReferenceAllelesTriDups
      The number of tripletons where the two reads matched the reference.
    • nAlternateAllelesTriDups

      public Integer nAlternateAllelesTriDups
      The number of tripletons where the two reads matched the alternate.
    • nMismatchingAllelesTriDups

      public Integer nMismatchingAllelesTriDups
      The number of tripletons where at least one of the reads didn't match either allele of the het site.
    • nReferenceReads

      public Integer nReferenceReads
      The number of reference alleles in the reads.
    • nAlternateReads

      public Integer nAlternateReads
      The number of alternate alleles in the reads.
    • nMismatchingUMIsInDiffBiDups

      public Integer nMismatchingUMIsInDiffBiDups
      The number of UMIs that are different within Bi-sets that come from different alleles.
    • nMatchingUMIsInDiffBiDups

      public Integer nMatchingUMIsInDiffBiDups
      The number of UMIs that are match within Bi-sets that come from different alleles.
    • nMismatchingUMIsInSameBiDups

      public Integer nMismatchingUMIsInSameBiDups
      The number of UMIs that are different within Bi-sets that come from the same alleles.
    • nMatchingUMIsInSameBiDups

      public Integer nMatchingUMIsInSameBiDups
      The number of UMIs that are match within Bi-sets that come from the same alleles.
    • nMismatchingUMIsInCoOrientedBiDups

      public Integer nMismatchingUMIsInCoOrientedBiDups
      The number of bi-sets with mismatching UMIs and same orientation.
    • nMismatchingUMIsInContraOrientedBiDups

      public Integer nMismatchingUMIsInContraOrientedBiDups
      The number of bi-sets with mismatching UMIs and opposite orientation.
    • nBadBarcodes

      public Integer nBadBarcodes
      The number of sets where the UMIs had poor quality bases and were not used for any comparisons.
    • nGoodBarcodes

      public Integer nGoodBarcodes
      the number of sets where the UMIs had good quality bases and were used for any comparisons.
    • biSiteHeterogeneityRate

      public Double biSiteHeterogeneityRate
      the rate of heterogeneity within doubleton sets.
    • triSiteHeterogeneityRate

      public Double triSiteHeterogeneityRate
      the rate of heterogeneity within tripleton sets
    • biSiteHomogeneityRate

      public Double biSiteHomogeneityRate
      the rate of homogeneity within doubleton sets.
    • triSiteHomogeneityRate

      public Double triSiteHomogeneityRate
      the rate of homogeneity within tripleton sets.
    • independentReplicationRateFromBiDups

      public Double independentReplicationRateFromBiDups
    • independentReplicationRateFromTriDups

      public Double independentReplicationRateFromTriDups
      The biological duplication rate (as a fraction of the duplicates sets) calculated from tripleton sets.
    • pSameUmiInIndependentBiDup

      public Double pSameUmiInIndependentBiDup
      When the alleles are different, we know that this is a biological duplication, thus we expect nearly all the UMIs to be different (allowing for equality due to chance). So we expect this to be near 1.
    • pSameAlleleWhenMismatchingUmi

      public Double pSameAlleleWhenMismatchingUmi
      When the UMIs mismatch, we expect about the same number of different alleles as the same (assuming that different UMI implies biological duplicate) thus, this value should be near 0.5
    • independentReplicationRateFromUmi

      public Double independentReplicationRateFromUmi
      Given the UMIs one can estimate the rate of biological duplication directly, as this would be the rate of having different UMIs in all duplicate sets. This is only a good estimate if the assumptions hold, for example if pSameUmiInIndependentBiDup is near 1.
    • replicationRateFromReplicateSets

      public Double replicationRateFromReplicateSets
      An estimate of the duplication rate that is based on the duplicate sets we observed.
  • Constructor Details

    • IndependentReplicateMetric

      public IndependentReplicateMetric()
  • Method Details

    • calculateDerivedFields

      public void calculateDerivedFields()
      Description copied from class: MergeableMetricBase
      Placeholder method that will calculate the derived fields from the other ones. Classes that are derived from non-trivial derived classes should consider calling super.calculateDerivedFields() as well. Fields whose value will change due to this method should be annotated with NoMergingKeepsValue.
      Overrides:
      calculateDerivedFields in class MergeableMetricBase