Package picard.analysis
Class TheoreticalSensitivityMetrics
java.lang.Object
htsjdk.samtools.metrics.MetricBase
picard.analysis.TheoreticalSensitivityMetrics
@DocumentedFeature(groupName="Metrics",
summary="Metrics")
public class TheoreticalSensitivityMetrics
extends htsjdk.samtools.metrics.MetricBase
TheoreticalSensitivityMetrics, are metrics calculated from TheoreticalSensitivity and parameters used in
the calculation.
These metrics are intended to estimate the achievable sensitivity (for a particular log odds threshold) of
somatic calls for a particular depth and base quality score distribution.
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Field Summary
FieldsModifier and TypeFieldDescriptiondouble
The allele fraction which theoretical sensitivity is calculated for.double
Log-likelihood ratio is used as a threshold to distinguish a positive site with a given allele fraction from HOM_REF.int
Number of samples drawn at each depth in the depth distribution.double
Estimation of sensitivity at a particular allele fraction.int
Phred-scaled value of 1-THEORETICAL_SENSITIVITY. -
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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ALLELE_FRACTION
public double ALLELE_FRACTIONThe allele fraction which theoretical sensitivity is calculated for. -
THEORETICAL_SENSITIVITY
public double THEORETICAL_SENSITIVITYEstimation of sensitivity at a particular allele fraction. -
THEORETICAL_SENSITIVITY_Q
public int THEORETICAL_SENSITIVITY_QPhred-scaled value of 1-THEORETICAL_SENSITIVITY. -
LOG_ODDS_THRESHOLD
public double LOG_ODDS_THRESHOLDLog-likelihood ratio is used as a threshold to distinguish a positive site with a given allele fraction from HOM_REF. -
SAMPLE_SIZE
public int SAMPLE_SIZENumber of samples drawn at each depth in the depth distribution. Larger values allow for increased precision at the cost of compute time.
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Constructor Details
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TheoreticalSensitivityMetrics
public TheoreticalSensitivityMetrics()
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