Class CalculateFingerprintMetrics


  • @DocumentedFeature
    public class CalculateFingerprintMetrics
    extends CommandLineProgram
    Calculates various metrics on a sample fingerprint, indicating whether the fingerprint satisfies the assumptions we have. For example, if too many sites are heterozygous, that would get flagged.
    • Field Detail

      • INPUT

        @Argument(shortName="I",
                  doc="One or more input files (SAM/BAM/CRAM or VCF).")
        public List<String> INPUT
      • OUTPUT

        @Argument(shortName="O",
                  doc="The output file to write (Metrics).")
        public File OUTPUT
      • HAPLOTYPE_MAP

        @Argument(shortName="H",
                  doc="The file lists a set of SNPs, optionally arranged in high-LD blocks, to be used for fingerprinting. See https://software.broadinstitute.org/gatk/documentation/article?id=9526 for details.")
        public File HAPLOTYPE_MAP
      • CALCULATE_BY

        @Argument(doc="Specificies which data-type should be used as the basic unit. Fingerprints from readgroups can be \"rolled-up\" to the LIBRARY, SAMPLE, or FILE level before being used. Fingerprints from VCF can be be examined by SAMPLE or FILE.")
        public CrosscheckMetric.DataType CALCULATE_BY
      • GENOTYPE_LOD_THRESHOLD

        @Argument(doc="LOD score threshold for considering a genotype to be definitive.")
        public final double GENOTYPE_LOD_THRESHOLD
        See Also:
        Constant Field Values
      • NUMBER_OF_SAMPLING

        @Argument(doc="Number of randomization trials for calculating the DISCRIMINATORY_POWER metric.")
        public final int NUMBER_OF_SAMPLING
        See Also:
        Constant Field Values
    • Constructor Detail

      • CalculateFingerprintMetrics

        public CalculateFingerprintMetrics()
    • Method Detail

      • doWork

        protected int doWork()
        Description copied from class: CommandLineProgram
        Do the work after command line has been parsed. RuntimeException may be thrown by this method, and are reported appropriately.
        Specified by:
        doWork in class CommandLineProgram
        Returns:
        program exit status.