Package picard.fingerprint
Class FingerprintMetrics
- java.lang.Object
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- htsjdk.samtools.metrics.MetricBase
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- picard.fingerprint.FingerprintMetrics
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@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 fromFingerprintingDetailMetrics
andFingerprintingSummaryMetrics
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.
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Field Summary
Fields Modifier and Type Field Description double
CHI_SQUARED_PVALUE
The Chi-squared pvalue of the observed counts vector relative to the expected counts, (3x2 table)double
CROSS_ENTROPY_LOD
The categorical cross entropy of the counts of genotypes relative to expected (big is bad)long
DEFINITE_GENOTYPES
Number of haplotypes that had enough evidence to make a definite genotype call (genotype LOD > Thresholddouble
DISCRIMINATORY_POWER
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_HET
Expected number of heterozygous callsdouble
EXPECTED_HOM_ALLELE1
Expected number of major allele homozygous callsdouble
EXPECTED_HOM_ALLELE2
Expected number of major allele homozygous callslong
HAPLOTYPES
Number of haplotypes examinedlong
HAPLOTYPES_WITH_EVIDENCE
Number of haplotypes that had evidence in the source filedouble
HET_CHI_SQUARED_PVALUE
The Chi-squared pvalue for the number of HETs and HOMs relative to the expected counts (2x2 table)double
HET_CROSS_ENTROPY_LOD
The categorical cross entropy of the counts of HETs and HOMs relative to the expected counts (big is bad)double
HOM_CHI_SQUARED_PVALUE
The Chi-squared pvalue forNUM_HOM_ALLELE1
andNUM_HOM_ALLELE2
relative to the expected counts (2x2 table)double
HOM_CROSS_ENTROPY_LOD
The categorical cross entropy ofNUM_HOM_ALLELE1
andNUM_HOM_ALLELE2
relative to the expected counts (big is bad)String
INFO
Additional information about the fingerprintdouble
LOD_SELF_CHECK
The fingerprinting LOD score this sample gets when compared to itself (big is good)double
LOG10_CHI_SQUARED_PVALUE
The log10 of the Chi-squared pvaluedouble
LOG10_HET_CHI_SQUARED_PVALUE
The log10 of the Chi-squared pvalue for the number of HETs and HOMsdouble
LOG10_HOM_CHI_SQUARED_PVALUE
The log10 of the Chi-squared pvalue forNUM_HOM_ALLELE1
andNUM_HOM_ALLELE2
long
NUM_HET
Number of heterozygous callslong
NUM_HOM_ALLELE1
Number of major allele homozygous callslong
NUM_HOM_ALLELE2
Number of minor allele homozygous callslong
NUM_HOM_ANY
Number of homozygous calls of either allele (might not be the sum ofNUM_HOM_ALLELE1
andNUM_HOM_ALLELE1
due to roundingString
SAMPLE_ALIAS
The Sample alias taken from RG header or #CHROME lineString
SOURCE
The originating file (if available) for this fingerprint
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Constructor Summary
Constructors Constructor Description FingerprintMetrics()
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Field Detail
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SAMPLE_ALIAS
public String SAMPLE_ALIAS
The Sample alias taken from RG header or #CHROME line
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SOURCE
public String SOURCE
The originating file (if available) for this fingerprint
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INFO
public String INFO
Additional information about the fingerprint
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HAPLOTYPES
public long HAPLOTYPES
Number of haplotypes examined
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HAPLOTYPES_WITH_EVIDENCE
public long HAPLOTYPES_WITH_EVIDENCE
Number of haplotypes that had evidence in the source file
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DEFINITE_GENOTYPES
public long DEFINITE_GENOTYPES
Number of haplotypes that had enough evidence to make a definite genotype call (genotype LOD > Threshold
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NUM_HOM_ALLELE1
public long NUM_HOM_ALLELE1
Number of major allele homozygous calls
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NUM_HOM_ALLELE2
public long NUM_HOM_ALLELE2
Number of minor allele homozygous calls
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NUM_HOM_ANY
public long NUM_HOM_ANY
Number of homozygous calls of either allele (might not be the sum ofNUM_HOM_ALLELE1
andNUM_HOM_ALLELE1
due to rounding
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NUM_HET
public long NUM_HET
Number of heterozygous calls
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EXPECTED_HOM_ALLELE1
public double EXPECTED_HOM_ALLELE1
Expected number of major allele homozygous calls
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EXPECTED_HOM_ALLELE2
public double EXPECTED_HOM_ALLELE2
Expected number of major allele homozygous calls
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EXPECTED_HET
public double EXPECTED_HET
Expected number of heterozygous calls
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CHI_SQUARED_PVALUE
public double CHI_SQUARED_PVALUE
The Chi-squared pvalue of the observed counts vector relative to the expected counts, (3x2 table)
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LOG10_CHI_SQUARED_PVALUE
public double LOG10_CHI_SQUARED_PVALUE
The log10 of the Chi-squared pvalue
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CROSS_ENTROPY_LOD
public double CROSS_ENTROPY_LOD
The categorical cross entropy of the counts of genotypes relative to expected (big is bad)
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HET_CHI_SQUARED_PVALUE
public double HET_CHI_SQUARED_PVALUE
The Chi-squared pvalue for the number of HETs and HOMs relative to the expected counts (2x2 table)
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LOG10_HET_CHI_SQUARED_PVALUE
public double LOG10_HET_CHI_SQUARED_PVALUE
The log10 of the Chi-squared pvalue for the number of HETs and HOMs
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HET_CROSS_ENTROPY_LOD
public double HET_CROSS_ENTROPY_LOD
The categorical cross entropy of the counts of HETs and HOMs relative to the expected counts (big is bad)
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HOM_CHI_SQUARED_PVALUE
public double HOM_CHI_SQUARED_PVALUE
The Chi-squared pvalue forNUM_HOM_ALLELE1
andNUM_HOM_ALLELE2
relative to the expected counts (2x2 table)
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LOG10_HOM_CHI_SQUARED_PVALUE
public double LOG10_HOM_CHI_SQUARED_PVALUE
The 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_LOD
The categorical cross entropy ofNUM_HOM_ALLELE1
andNUM_HOM_ALLELE2
relative to the expected counts (big is bad)
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LOD_SELF_CHECK
public double LOD_SELF_CHECK
The fingerprinting LOD score this sample gets when compared to itself (big is good)
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DISCRIMINATORY_POWER
public double DISCRIMINATORY_POWER
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. (big is good.)
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