Package picard.vcf

Class SplitVcfs


  • @DocumentedFeature
    public class SplitVcfs
    extends CommandLineProgram
    Splits the input VCF file into two, one for indels and one for SNPs. The headers of the two output files will be identical.

    An index file is created for the output file by default. Using an output file name with a ".gz" extension will create gzip-compressed output.

    • Field Detail

      • INPUT

        @Argument(shortName="I",
                  doc="The VCF or BCF input file")
        public File INPUT
      • SNP_OUTPUT

        @Argument(doc="The VCF or BCF file to which SNP records should be written. The file format is determined by file extension.")
        public File SNP_OUTPUT
      • INDEL_OUTPUT

        @Argument(doc="The VCF or BCF file to which indel records should be written. The file format is determined by file extension.")
        public File INDEL_OUTPUT
      • SEQUENCE_DICTIONARY

        @Argument(shortName="D",
                  doc="The index sequence dictionary to use instead of the sequence dictionaries in the input files",
                  optional=true)
        public File SEQUENCE_DICTIONARY
      • STRICT

        @Argument(doc="If true an exception will be thrown if an event type other than SNP or indel is encountered")
        public Boolean STRICT
    • Constructor Detail

      • SplitVcfs

        public SplitVcfs()
    • 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.