Package picard.vcf

Class SortVcf


  • @DocumentedFeature
    public class SortVcf
    extends CommandLineProgram
    Sorts one or more VCF files according to the order of the contigs in the header/sequence dictionary and then by coordinate. Can accept an external dictionary. If no external dictionary is supplied, multiple inputs' headers must have the same sequence dictionaries
    • Field Detail

      • INPUT

        @Argument(shortName="I",
                  doc="Input VCF(s) to be sorted. Multiple inputs must have the same sample names (in order)")
        public List<File> INPUT
      • OUTPUT

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

        @Argument(shortName="SD",
                  optional=true)
        public File SEQUENCE_DICTIONARY
    • Constructor Detail

      • SortVcf

        public SortVcf()
    • 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.