Package picard.analysis
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.
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Field Summary
FieldsModifier and TypeFieldDescriptionThe 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 -
Method Summary
Methods inherited from class htsjdk.samtools.metrics.MetricBase
equals, hashCode, toString
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Field Details
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READ_GROUP
The sequencing read group from which sequence data was fingerprinted. -
SAMPLE
The name of the sample who's genotypes the sequence data was compared to. -
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
The possible alleles for the SNP. -
CHROM
The chromosome on which the SNP resides. -
POSITION
public int POSITIONThe position of the SNP on the chromosome. -
EXPECTED_GENOTYPE
The expected genotype of the sample at the SNP locus. -
OBSERVED_GENOTYPE
The most likely genotype given the observed evidence at the SNP locus in the sequencing data. -
LOD
public double LODThe LOD score for OBSERVED_GENOTYPE vs. the next most likely genotype in the sequencing data. -
OBS_A
public int OBS_AThe number of observations of the first, or A, allele of the SNP in the sequencing data. -
OBS_B
public int OBS_BThe number of observations of the second, or B, allele of the SNP in the sequencing data.
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Constructor Details
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FingerprintingDetailMetrics
public FingerprintingDetailMetrics()
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