Package picard.fingerprint

Class FingerprintMetrics

  • 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 Detail

      • SAMPLE_ALIAS

        public String SAMPLE_ALIAS
        The Sample alias taken from RG header or #CHROME line

      • SOURCE

        public String SOURCE
        The originating file (if available) for this fingerprint

      • INFO

        public String INFO
        Additional information about the fingerprint

      • HAPLOTYPES

        public long HAPLOTYPES
        Number of haplotypes examined

      • HAPLOTYPES_WITH_EVIDENCE

        public long HAPLOTYPES_WITH_EVIDENCE
        Number of haplotypes that had evidence in the source file

      • DEFINITE_GENOTYPES

        public long DEFINITE_GENOTYPES
        Number of haplotypes that had enough evidence to make a definite genotype call (genotype LOD > Threshold

      • NUM_HOM_ALLELE1

        public long NUM_HOM_ALLELE1
        Number of major allele homozygous calls

      • NUM_HOM_ALLELE2

        public long NUM_HOM_ALLELE2
        Number of minor allele homozygous calls

      • NUM_HOM_ANY

        public long NUM_HOM_ANY
        Number of homozygous calls of either allele (might not be the sum of NUM_HOM_ALLELE1 and NUM_HOM_ALLELE1 due to rounding

      • NUM_HET

        public long NUM_HET
        Number of heterozygous calls

      • EXPECTED_HOM_ALLELE1

        public double EXPECTED_HOM_ALLELE1
        Expected number of major allele homozygous calls

      • EXPECTED_HOM_ALLELE2

        public double EXPECTED_HOM_ALLELE2
        Expected number of major allele homozygous calls

      • EXPECTED_HET

        public double EXPECTED_HET
        Expected number of heterozygous calls

      • CHI_SQUARED_PVALUE

        public double CHI_SQUARED_PVALUE
        The Chi-squared pvalue of the observed counts vector relative to the expected counts, (3x2 table)

      • LOG10_CHI_SQUARED_PVALUE

        public double LOG10_CHI_SQUARED_PVALUE
        The log10 of the Chi-squared pvalue

      • CROSS_ENTROPY_LOD

        public double CROSS_ENTROPY_LOD
        The categorical cross entropy of the counts of genotypes relative to expected (big is bad)

      • 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)

      • 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

      • 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)

      • HOM_CHI_SQUARED_PVALUE

        public double HOM_CHI_SQUARED_PVALUE
        The Chi-squared pvalue for NUM_HOM_ALLELE1 and NUM_HOM_ALLELE2 relative to the expected counts (2x2 table)

      • LOG10_HOM_CHI_SQUARED_PVALUE

        public double LOG10_HOM_CHI_SQUARED_PVALUE
        The log10 of the Chi-squared pvalue for NUM_HOM_ALLELE1 and NUM_HOM_ALLELE2

      • HOM_CROSS_ENTROPY_LOD

        public double HOM_CROSS_ENTROPY_LOD
        The categorical cross entropy of NUM_HOM_ALLELE1 and NUM_HOM_ALLELE2 relative to the expected counts (big is bad)

      • LOD_SELF_CHECK

        public double LOD_SELF_CHECK
        The fingerprinting LOD score this sample gets when compared to itself (big is good)

      • 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.)

    • Constructor Detail

      • FingerprintMetrics

        public FingerprintMetrics()