Package picard.analysis
Class FingerprintingSummaryMetrics
- java.lang.Object
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- htsjdk.samtools.metrics.MetricBase
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- picard.analysis.FingerprintingSummaryMetrics
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@DocumentedFeature(groupName="Metrics", summary="Metrics") public class FingerprintingSummaryMetrics extends htsjdk.samtools.metrics.MetricBase
Summary fingerprinting metrics and statistics about the comparison of the sequence data from a single read group (lane or index within a lane) vs. a set of known genotypes for the expected sample.
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Field Summary
Fields Modifier and Type Field Description int
HAPLOTYPES_CONFIDENTLY_CHECKED
The subset of genotyped haplotypes for which there was sufficient sequence data to confidently genotype the haplotype.int
HAPLOTYPES_CONFIDENTLY_MATCHING
The subset of confidently checked haplotypes that match the expected genotypes.int
HAPLOTYPES_WITH_GENOTYPES
The number of haplotypes that had expected genotypes to compare to.int
HET_AS_HOM
num of hets, observed as homs with LOD > thresholdint
HOM_AS_HET
num of homs, observed as hets with LOD > thresholdint
HOM_AS_OTHER_HOM
num of homs, observed as other homs with LOD > thresholddouble
LL_EXPECTED_SAMPLE
The Log Likelihood of the sequence data given the expected sample's genotypes.double
LL_RANDOM_SAMPLE
The Log Likelihood of the sequence data given a random sample from the human population.double
LOD_EXPECTED_SAMPLE
The LOD for Expected Sample vs.String
READ_GROUP
The read group from which sequence data was drawn for comparison.String
SAMPLE
The sample whose known genotypes the sequence data was compared to.
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Constructor Summary
Constructors Constructor Description FingerprintingSummaryMetrics()
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Field Detail
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READ_GROUP
public String READ_GROUP
The read group from which sequence data was drawn for comparison.
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SAMPLE
public String SAMPLE
The sample whose known genotypes the sequence data was compared to.
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LL_EXPECTED_SAMPLE
public double LL_EXPECTED_SAMPLE
The Log Likelihood of the sequence data given the expected sample's genotypes.
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LL_RANDOM_SAMPLE
public double LL_RANDOM_SAMPLE
The Log Likelihood of the sequence data given a random sample from the human population.
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LOD_EXPECTED_SAMPLE
public double LOD_EXPECTED_SAMPLE
The LOD for Expected Sample vs. Random Sample. A positive LOD indicates that the sequence data is more likely to come from the expected sample vs. a random sample from the population, by LOD logs. I.e. a value of 6 indicates that the sequence data is 1,000,000 more likely to come from the expected sample than from a random sample. A negative LOD indicates the reverse - that the sequence data is more likely to come from a random sample than from the expected sample.
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HAPLOTYPES_WITH_GENOTYPES
public int HAPLOTYPES_WITH_GENOTYPES
The number of haplotypes that had expected genotypes to compare to.
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HAPLOTYPES_CONFIDENTLY_CHECKED
public int HAPLOTYPES_CONFIDENTLY_CHECKED
The subset of genotyped haplotypes for which there was sufficient sequence data to confidently genotype the haplotype. Note: all haplotypes with sequence coverage contribute to the LOD score, even if they cannot be "confidently checked" individually.
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HAPLOTYPES_CONFIDENTLY_MATCHING
public int HAPLOTYPES_CONFIDENTLY_MATCHING
The subset of confidently checked haplotypes that match the expected genotypes.
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HET_AS_HOM
public int HET_AS_HOM
num of hets, observed as homs with LOD > threshold
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HOM_AS_HET
public int HOM_AS_HET
num of homs, observed as hets with LOD > threshold
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HOM_AS_OTHER_HOM
public int HOM_AS_OTHER_HOM
num of homs, observed as other homs with LOD > threshold
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