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 Details

    • INPUT

      @Argument(shortName="I", doc="The VCF or BCF input file") public PicardHtsPath 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 PicardHtsPath 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 Details

    • SplitVcfs

      public SplitVcfs()
  • 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.