Package picard.analysis
Class TheoreticalSensitivityMetrics
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- htsjdk.samtools.metrics.MetricBase
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- picard.analysis.TheoreticalSensitivityMetrics
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@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
Fields Modifier and Type Field Description double
ALLELE_FRACTION
The allele fraction which theoretical sensitivity is calculated for.double
LOG_ODDS_THRESHOLD
Log-likelihood ratio is used as a threshold to distinguish a positive site with a given allele fraction from HOM_REF.int
SAMPLE_SIZE
Number of samples drawn at each depth in the depth distribution.double
THEORETICAL_SENSITIVITY
Estimation of sensitivity at a particular allele fraction.int
THEORETICAL_SENSITIVITY_Q
Phred-scaled value of 1-THEORETICAL_SENSITIVITY.
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Constructor Summary
Constructors Constructor Description TheoreticalSensitivityMetrics()
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Field Detail
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ALLELE_FRACTION
public double ALLELE_FRACTION
The allele fraction which theoretical sensitivity is calculated for.
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THEORETICAL_SENSITIVITY
public double THEORETICAL_SENSITIVITY
Estimation of sensitivity at a particular allele fraction.
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THEORETICAL_SENSITIVITY_Q
public int THEORETICAL_SENSITIVITY_Q
Phred-scaled value of 1-THEORETICAL_SENSITIVITY.
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LOG_ODDS_THRESHOLD
public double LOG_ODDS_THRESHOLD
Log-likelihood ratio is used as a threshold to distinguish a positive site with a given allele fraction from HOM_REF.
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SAMPLE_SIZE
public int SAMPLE_SIZE
Number 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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