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 Detail

      • 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 Detail

      • VcfToAdpc

        public VcfToAdpc()
    • 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.