Package picard.vcf

Class GatherVcfs


@DocumentedFeature public class GatherVcfs extends CommandLineProgram
Simple little class that combines multiple VCFs that have exactly the same set of samples and nonoverlapping sets of loci.
  • Field Details

    • INPUT

      @Argument(shortName="I", doc="Input VCF file(s).") public List<htsjdk.io.HtsPath> INPUT
    • OUTPUT

      @Argument(shortName="O", doc="Output VCF file.") public File OUTPUT
    • COMMENT

      @Argument(doc="Comment(s) to include in the merged output file\'s header.", optional=true, shortName="CO") public List<String> COMMENT
    • REORDER_INPUT_BY_FIRST_VARIANT

      @Argument(doc="If \'true\' the program will reorder INPUT according to the genomic location of the first variant in each file. this is useful since the order of variants in each file in INPUT come from non overlapping regions but the order of the files in INPUT is untrusted.", optional=true, shortName="RI") public boolean REORDER_INPUT_BY_FIRST_VARIANT
  • Constructor Details

    • GatherVcfs

      public GatherVcfs()
  • 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.