Package picard.vcf

Class UpdateVcfSequenceDictionary

java.lang.Object
picard.cmdline.CommandLineProgram
picard.vcf.UpdateVcfSequenceDictionary

@DocumentedFeature public class UpdateVcfSequenceDictionary extends CommandLineProgram
Takes a VCF file and a Sequence Dictionary (from a variety of file types) and updates the Sequence Dictionary in VCF.
  • Field Details

    • INPUT

      @Argument(shortName="I", doc="Input VCF") public File INPUT
    • OUTPUT

      @Argument(shortName="O", doc="Output VCF to be written.") public File OUTPUT
    • SEQUENCE_DICTIONARY

      @Argument(shortName="SD", doc="A Sequence Dictionary (can be read from one of the following file types (SAM, BAM, VCF, BCF, Interval List, Fasta, or Dict)") public File SEQUENCE_DICTIONARY
  • Constructor Details

    • UpdateVcfSequenceDictionary

      public UpdateVcfSequenceDictionary()
  • 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.