Package picard.analysis
Class FingerprintingSummaryMetrics
java.lang.Object
htsjdk.samtools.metrics.MetricBase
picard.analysis.FingerprintingSummaryMetrics
@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
FieldsModifier and TypeFieldDescriptionint
The subset of genotyped haplotypes for which there was sufficient sequence data to confidently genotype the haplotype.int
The subset of confidently checked haplotypes that match the expected genotypes.int
The number of haplotypes that had expected genotypes to compare to.int
num of hets, observed as homs with LOD > thresholdint
num of homs, observed as hets with LOD > thresholdint
num of homs, observed as other homs with LOD > thresholddouble
The Log Likelihood of the sequence data given the expected sample's genotypes.double
The Log Likelihood of the sequence data given a random sample from the human population.double
The LOD for Expected Sample vs.The read group from which sequence data was drawn for comparison.The sample whose known genotypes the sequence data was compared to. -
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 read group from which sequence data was drawn for comparison. -
SAMPLE
The sample whose known genotypes the sequence data was compared to. -
LL_EXPECTED_SAMPLE
public double LL_EXPECTED_SAMPLEThe Log Likelihood of the sequence data given the expected sample's genotypes. -
LL_RANDOM_SAMPLE
public double LL_RANDOM_SAMPLEThe Log Likelihood of the sequence data given a random sample from the human population. -
LOD_EXPECTED_SAMPLE
public double LOD_EXPECTED_SAMPLEThe 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. -
HAPLOTYPES_WITH_GENOTYPES
public int HAPLOTYPES_WITH_GENOTYPESThe number of haplotypes that had expected genotypes to compare to. -
HAPLOTYPES_CONFIDENTLY_CHECKED
public int HAPLOTYPES_CONFIDENTLY_CHECKEDThe 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. -
HAPLOTYPES_CONFIDENTLY_MATCHING
public int HAPLOTYPES_CONFIDENTLY_MATCHINGThe subset of confidently checked haplotypes that match the expected genotypes. -
HET_AS_HOM
public int HET_AS_HOMnum of hets, observed as homs with LOD > threshold -
HOM_AS_HET
public int HOM_AS_HETnum of homs, observed as hets with LOD > threshold -
HOM_AS_OTHER_HOM
public int HOM_AS_OTHER_HOMnum of homs, observed as other homs with LOD > threshold
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Constructor Details
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FingerprintingSummaryMetrics
public FingerprintingSummaryMetrics()
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