Class 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
      String CHROM
      The chromosome on which the SNP resides.
      String EXPECTED_GENOTYPE
      The expected genotype of the sample at the SNP locus.
      double LOD
      The LOD score for OBSERVED_GENOTYPE vs.
      int OBS_A
      The number of observations of the first, or A, allele of the SNP in the sequencing data.
      int OBS_B
      The number of observations of the second, or B, allele of the SNP in the sequencing data.
      String OBSERVED_GENOTYPE
      The most likely genotype given the observed evidence at the SNP locus in the sequencing data.
      int POSITION
      The position of the SNP on the chromosome.
      String READ_GROUP
      The sequencing read group from which sequence data was fingerprinted.
      String SAMPLE
      The name of the sample who's genotypes the sequence data was compared to.
      String SNP
      The name of a representative SNP within the haplotype that was compared.
      String SNP_ALLELES
      The possible alleles for the SNP.
    • Field Detail

      • 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 Detail

      • FingerprintingDetailMetrics

        public FingerprintingDetailMetrics()