Class FingerprintingDetailMetrics

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

@DocumentedFeature(groupName="Metrics", summary="Metrics") public class FingerprintingDetailMetrics extends htsjdk.samtools.metrics.MetricBase
Detailed metrics about an individual SNP/Haplotype comparison within a fingerprint comparison.
  • Field Summary

    Fields
    Modifier and Type
    Field
    Description
    The chromosome on which the SNP resides.
    The expected genotype of the sample at the SNP locus.
    double
    The LOD score for OBSERVED_GENOTYPE vs.
    int
    The number of observations of the first, or A, allele of the SNP in the sequencing data.
    int
    The number of observations of the second, or B, allele of the SNP in the sequencing data.
    The most likely genotype given the observed evidence at the SNP locus in the sequencing data.
    int
    The position of the SNP on the chromosome.
    The sequencing read group from which sequence data was fingerprinted.
    The name of the sample who's genotypes the sequence data was compared to.
    The name of a representative SNP within the haplotype that was compared.
    The possible alleles for the SNP.
  • Constructor Summary

    Constructors
    Constructor
    Description
     
  • 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

    • READ_GROUP

      public String READ_GROUP
      The sequencing read group from which sequence data was fingerprinted.
    • SAMPLE

      public String SAMPLE
      The name of the sample who's genotypes the sequence data was compared to.
    • SNP

      public String SNP
      The name of a representative SNP within the haplotype that was compared. Will usually be the exact SNP that was genotyped externally.
    • SNP_ALLELES

      public String SNP_ALLELES
      The possible alleles for the SNP.
    • CHROM

      public String CHROM
      The chromosome on which the SNP resides.
    • POSITION

      public int POSITION
      The position of the SNP on the chromosome.
    • EXPECTED_GENOTYPE

      public String EXPECTED_GENOTYPE
      The expected genotype of the sample at the SNP locus.
    • OBSERVED_GENOTYPE

      public String OBSERVED_GENOTYPE
      The most likely genotype given the observed evidence at the SNP locus in the sequencing data.
    • LOD

      public double LOD
      The LOD score for OBSERVED_GENOTYPE vs. the next most likely genotype in the sequencing data.
    • OBS_A

      public int OBS_A
      The number of observations of the first, or A, allele of the SNP in the sequencing data.
    • OBS_B

      public int OBS_B
      The number of observations of the second, or B, allele of the SNP in the sequencing data.
  • Constructor Details

    • FingerprintingDetailMetrics

      public FingerprintingDetailMetrics()