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 totally discrete sets of loci.
    • Field Detail

      • INPUT

        @Argument(shortName="I",
                  doc="Input VCF file(s).")
        public List<File> 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 Detail

      • GatherVcfs

        public GatherVcfs()
    • Method Detail

      • 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.