picard.analysis

Class TheoreticalSensitivityMetrics

java.lang.Object

htsjdk.samtools.metrics.MetricBase

picard.analysis.TheoreticalSensitivityMetrics

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.

Field Summary

Fields

Modifier and Type	Field and 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.

Constructor Summary

Constructors

Constructor and Description
TheoreticalSensitivityMetrics()

Method Summary

Methods inherited from class htsjdk.samtools.metrics.MetricBase

equals, hashCode, toString

Methods inherited from class java.lang.Object

clone, finalize, getClass, notify, notifyAll, wait, wait, wait

Field Detail

ALLELE_FRACTION

public double ALLELE_FRACTION

The allele fraction which theoretical sensitivity is calculated for.

THEORETICAL_SENSITIVITY

public double THEORETICAL_SENSITIVITY

Estimation of sensitivity at a particular allele fraction.

THEORETICAL_SENSITIVITY_Q

public int THEORETICAL_SENSITIVITY_Q

Phred-scaled value of 1-THEORETICAL_SENSITIVITY.

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.

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.

Constructor Detail

TheoreticalSensitivityMetrics

public TheoreticalSensitivityMetrics()