Class IdentifyContaminant


  • public class IdentifyContaminant
    extends CommandLineProgram
    Program to create a fingerprint for the contaminating sample when the level of contamination is both known and uniform in the genome.
    • 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

      • 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.