Package picard.analysis
Class FingerprintingDetailMetrics
- java.lang.Object
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- htsjdk.samtools.metrics.MetricBase
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- picard.analysis.FingerprintingDetailMetrics
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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
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.
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Constructor Summary
Constructors Constructor Description FingerprintingDetailMetrics()
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Field Detail
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READ_GROUP
public String READ_GROUP
The sequencing read group from which sequence data was fingerprinted.
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SAMPLE
public String SAMPLE
The name of the sample who's genotypes the sequence data was compared to.
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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.
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SNP_ALLELES
public String SNP_ALLELES
The possible alleles for the SNP.
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CHROM
public String CHROM
The chromosome on which the SNP resides.
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POSITION
public int POSITION
The position of the SNP on the chromosome.
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EXPECTED_GENOTYPE
public String EXPECTED_GENOTYPE
The expected genotype of the sample at the SNP locus.
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OBSERVED_GENOTYPE
public String OBSERVED_GENOTYPE
The most likely genotype given the observed evidence at the SNP locus in the sequencing data.
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LOD
public double LOD
The LOD score for OBSERVED_GENOTYPE vs. the next most likely genotype in the sequencing data.
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OBS_A
public int OBS_A
The number of observations of the first, or A, allele of the SNP in the sequencing data.
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OBS_B
public int OBS_B
The number of observations of the second, or B, allele of the SNP in the sequencing data.
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