Package picard.vcf

Class 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 Detail

      • 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 Detail

      • UpdateVcfSequenceDictionary

        public UpdateVcfSequenceDictionary()
    • Method Detail

      • main

        public static void main​(String[] args)
      • 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.