Class ExtractFingerprint

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

public class ExtractFingerprint 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/BAM/CRAM 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://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. A non-zero value will cause the program to provide a better estimate of the fingerprint in the presence of contaminating reads", 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>\" is used. If argument EXTRACT_CONTAMINATION=true the resulting samplename will be \"<SAMPLE>-contamination\" (if not provided).", 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_CONTAMINATION

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

    • ExtractFingerprint

      public ExtractFingerprint()
  • 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.