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 Details

    • 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 Details

    • SortVcf

      public SortVcf()
  • 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.