Package picard.fingerprint

Class IdentifyContaminant

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

    • INPUT

      @Argument(shortName="I", doc="Input SAM or BAM file.") public String 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://gatk.broadinstitute.org/hc/en-us/articles/360035531672-Haplotype-map-format 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>, using the SM value from the SAM header.") public boolean EXTRACT_CONTAMINATED

    • 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

    • IdentifyContaminant

      public IdentifyContaminant()

  • Method Details

    • 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.