Class CalculateFingerprintMetrics

java.lang.Object
picard.cmdline.CommandLineProgram
picard.fingerprint.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 Details

    • 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:
    • NUMBER_OF_SAMPLING

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

      @Hidden @Argument(doc="When true code will check for readability on input files (this can be slow on cloud access)") public boolean TEST_INPUT_READABILITY
  • Constructor Details

    • CalculateFingerprintMetrics

      public CalculateFingerprintMetrics()
  • Method Details

    • 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.
    • getFingerprintMetrics

      public FingerprintMetrics getFingerprintMetrics(Fingerprint fingerprint)