Package picard.fingerprint
Class FingerprintMetrics
java.lang.Object
htsjdk.samtools.metrics.MetricBase
picard.fingerprint.FingerprintMetrics
@DocumentedFeature(groupName="Metrics",
summary="Metrics")
public class FingerprintMetrics
extends htsjdk.samtools.metrics.MetricBase
Class for holding metrics on a single fingerprint.
Note: this is distinct from
FingerprintingDetailMetrics
and
FingerprintingSummaryMetrics
in that it is calculated on a single fingerprint,
and attempts to describe how likely that fingerprint is to have arisen from an actual sample
as opposed to having artifacts such as contamination, or strong bias towards homozygous genotypes.
Several tests use "expected" genotype distribution based on the allele frequency stored in the haplotype-database
file that is used, and assuming Hardy-Weinberg equilibrium.
Please see the FingerprintMetrics definitions
http://broadinstitute.github.io/picard/picard-metric-definitions.html#FingerprintMetrics " +
for a complete description of the metrics produced by this tool.-
Field Summary
FieldsModifier and TypeFieldDescriptiondouble
The Chi-squared pvalue of the observed counts vector relative to the expected counts, (3x2 table)double
The categorical cross entropy of the counts of genotypes relative to expected (big is bad)long
Number of haplotypes that had enough evidence to make a definite genotype call (genotype LOD > Thresholddouble
The difference in fingerprinting LOD between LOD_SELF_CHECK and the LOD score found when fingerprinting it against a random permutation of the probablity vectors (PLs) in each of the haplotypes.double
Expected number of heterozygous callsdouble
Expected number of major allele homozygous callsdouble
Expected number of major allele homozygous callslong
Number of haplotypes examinedlong
Number of haplotypes that had evidence in the source filedouble
The Chi-squared pvalue for the number of HETs and HOMs relative to the expected counts (2x2 table)double
The categorical cross entropy of the counts of HETs and HOMs relative to the expected counts (big is bad)double
The Chi-squared pvalue forNUM_HOM_ALLELE1
andNUM_HOM_ALLELE2
relative to the expected counts (2x2 table)double
The categorical cross entropy ofNUM_HOM_ALLELE1
andNUM_HOM_ALLELE2
relative to the expected counts (big is bad)Additional information about the fingerprintdouble
The fingerprinting LOD score this sample gets when compared to itself (big is good)double
The log10 of the Chi-squared pvaluedouble
The log10 of the Chi-squared pvalue for the number of HETs and HOMsdouble
The log10 of the Chi-squared pvalue forNUM_HOM_ALLELE1
andNUM_HOM_ALLELE2
long
Number of heterozygous callslong
Number of major allele homozygous callslong
Number of minor allele homozygous callslong
Number of homozygous calls of either allele (might not be the sum ofNUM_HOM_ALLELE1
andNUM_HOM_ALLELE1
due to roundingThe Sample alias taken from RG header or #CHROME lineThe originating file (if available) for this fingerprint -
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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SAMPLE_ALIAS
The Sample alias taken from RG header or #CHROME line -
SOURCE
The originating file (if available) for this fingerprint -
INFO
Additional information about the fingerprint -
HAPLOTYPES
public long HAPLOTYPESNumber of haplotypes examined -
HAPLOTYPES_WITH_EVIDENCE
public long HAPLOTYPES_WITH_EVIDENCENumber of haplotypes that had evidence in the source file -
DEFINITE_GENOTYPES
public long DEFINITE_GENOTYPESNumber of haplotypes that had enough evidence to make a definite genotype call (genotype LOD > Threshold -
NUM_HOM_ALLELE1
public long NUM_HOM_ALLELE1Number of major allele homozygous calls -
NUM_HOM_ALLELE2
public long NUM_HOM_ALLELE2Number of minor allele homozygous calls -
NUM_HOM_ANY
public long NUM_HOM_ANYNumber of homozygous calls of either allele (might not be the sum ofNUM_HOM_ALLELE1
andNUM_HOM_ALLELE1
due to rounding -
NUM_HET
public long NUM_HETNumber of heterozygous calls -
EXPECTED_HOM_ALLELE1
public double EXPECTED_HOM_ALLELE1Expected number of major allele homozygous calls -
EXPECTED_HOM_ALLELE2
public double EXPECTED_HOM_ALLELE2Expected number of major allele homozygous calls -
EXPECTED_HET
public double EXPECTED_HETExpected number of heterozygous calls -
CHI_SQUARED_PVALUE
public double CHI_SQUARED_PVALUEThe Chi-squared pvalue of the observed counts vector relative to the expected counts, (3x2 table) -
LOG10_CHI_SQUARED_PVALUE
public double LOG10_CHI_SQUARED_PVALUEThe log10 of the Chi-squared pvalue -
CROSS_ENTROPY_LOD
public double CROSS_ENTROPY_LODThe categorical cross entropy of the counts of genotypes relative to expected (big is bad) -
HET_CHI_SQUARED_PVALUE
public double HET_CHI_SQUARED_PVALUEThe Chi-squared pvalue for the number of HETs and HOMs relative to the expected counts (2x2 table) -
LOG10_HET_CHI_SQUARED_PVALUE
public double LOG10_HET_CHI_SQUARED_PVALUEThe log10 of the Chi-squared pvalue for the number of HETs and HOMs -
HET_CROSS_ENTROPY_LOD
public double HET_CROSS_ENTROPY_LODThe categorical cross entropy of the counts of HETs and HOMs relative to the expected counts (big is bad) -
HOM_CHI_SQUARED_PVALUE
public double HOM_CHI_SQUARED_PVALUEThe Chi-squared pvalue forNUM_HOM_ALLELE1
andNUM_HOM_ALLELE2
relative to the expected counts (2x2 table) -
LOG10_HOM_CHI_SQUARED_PVALUE
public double LOG10_HOM_CHI_SQUARED_PVALUEThe log10 of the Chi-squared pvalue forNUM_HOM_ALLELE1
andNUM_HOM_ALLELE2
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HOM_CROSS_ENTROPY_LOD
public double HOM_CROSS_ENTROPY_LODThe categorical cross entropy ofNUM_HOM_ALLELE1
andNUM_HOM_ALLELE2
relative to the expected counts (big is bad) -
LOD_SELF_CHECK
public double LOD_SELF_CHECKThe fingerprinting LOD score this sample gets when compared to itself (big is good) -
DISCRIMINATORY_POWER
public double DISCRIMINATORY_POWERThe difference in fingerprinting LOD between LOD_SELF_CHECK and the LOD score found when fingerprinting it against a random permutation of the probablity vectors (PLs) in each of the haplotypes. (big is good.)
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Constructor Details
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FingerprintMetrics
public FingerprintMetrics()
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