picard.analysis

Class FingerprintingSummaryMetrics

java.lang.Object

htsjdk.samtools.metrics.MetricBase

picard.analysis.FingerprintingSummaryMetrics

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.

Author:

Tim Fennell

Field Summary

Fields

Modifier and Type	Field and 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 > threshold
int	HOM_AS_HET num of homs, observed as hets with LOD > threshold
int	HOM_AS_OTHER_HOM num of homs, observed as other homs with LOD > threshold
double	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.
java.lang.String	READ_GROUP The read group from which sequence data was drawn for comparison.
java.lang.String	SAMPLE The sample whose known genotypes the sequence data was compared to.

Constructor Summary

Constructors

Constructor and Description
FingerprintingSummaryMetrics()

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

READ_GROUP

public java.lang.String READ_GROUP

The read group from which sequence data was drawn for comparison.

SAMPLE

public java.lang.String SAMPLE

The sample whose known genotypes the sequence data was compared to.

LL_EXPECTED_SAMPLE

public double LL_EXPECTED_SAMPLE

The Log Likelihood of the sequence data given the expected sample's genotypes.

LL_RANDOM_SAMPLE

public double LL_RANDOM_SAMPLE

The Log Likelihood of the sequence data given a random sample from the human population.

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.

HAPLOTYPES_WITH_GENOTYPES

public int HAPLOTYPES_WITH_GENOTYPES

The number of haplotypes that had expected genotypes to compare to.

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.

HAPLOTYPES_CONFIDENTLY_MATCHING

public int HAPLOTYPES_CONFIDENTLY_MATCHING

The subset of confidently checked haplotypes that match the expected genotypes.

HET_AS_HOM

public int HET_AS_HOM

num of hets, observed as homs with LOD > threshold

HOM_AS_HET

public int HOM_AS_HET

num of homs, observed as hets with LOD > threshold

HOM_AS_OTHER_HOM

public int HOM_AS_OTHER_HOM

num of homs, observed as other homs with LOD > threshold

Constructor Detail

FingerprintingSummaryMetrics

public FingerprintingSummaryMetrics()