Field Detail

• INPUT

  @Argument(shortName="I",
            doc="Input SAM or BAM file.")
  public File INPUT

• OUTPUT

  @Argument(shortName="O",
            doc="Output fingerprint file (VCF).")
  public File OUTPUT

• HAPLOTYPE_MAP

  @Argument(shortName="H",
            doc="A file of haplotype information. 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

• CONTAMINATION

  @Argument(shortName="C",
            doc="A value of estimated contamination in the input. ",
            minValue=0.0,
            maxValue=1.0)
  public double CONTAMINATION

• SAMPLE_ALIAS

  @Argument(doc="The sample alias to associate with the resulting fingerprint. When null, <SAMPLE> is extracted from the input file and \"<SAMPLE>-contamination\" is used.",
            optional=true)
  public String SAMPLE_ALIAS

• LOCUS_MAX_READS

  @Argument(doc="The maximum number of reads to use as evidence for any given locus. This is provided as a way to limit the effect that any given locus may have.")
  public int LOCUS_MAX_READS

• EXTRACT_CONTAMINATED

  @Argument(doc="Extract a fingerprint for the contaminated sample (instead of the contaminant). Setting to true changes the effect of SAMPLE_ALIAS when null. It names the sample in the VCF <SAMPLE>-contaminated, using the SM value from the SAM header.")
  public boolean EXTRACT_CONTAMINATED

Constructor Detail

• IdentifyContaminant

  public IdentifyContaminant()

Method Detail

• requiresReference

  protected boolean requiresReference()

  Overrides:

  requiresReference in class CommandLineProgram

• 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.