Package picard.arrays

Class VcfToAdpc


@DocumentedFeature public class VcfToAdpc extends CommandLineProgram
A simple program to convert a Genotyping Arrays VCF to an ADPC file (Illumina intensity data file).
  • Field Details

    • VCF

      @Argument(doc="One or more VCF files containing array intensity data.") public List<File> VCF
    • OUTPUT

      @Argument(shortName="O", doc="The output (adpc.bin) file to write.") public File OUTPUT
    • SAMPLES_FILE

      @Argument(shortName="SF", doc="A text file into which the names of the samples will be written. These will be in the same order as the data in the adpc.bin file.") public File SAMPLES_FILE
    • NUM_MARKERS_FILE

      @Argument(shortName="NMF", doc="A text file into which the number of loci in the VCF will be written. This is useful for calling verifyIDIntensity.") public File NUM_MARKERS_FILE
  • Constructor Details

    • VcfToAdpc

      public VcfToAdpc()
  • 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.