Class LiftOverHaplotypeMap

java.lang.Object
picard.cmdline.CommandLineProgram
picard.fingerprint.LiftOverHaplotypeMap

public class LiftOverHaplotypeMap extends CommandLineProgram
Liftover SNPs in HaplotypeMaps from one reference to another
  • Field Details

    • INPUT

      @Argument(doc="Haplotype database to be lifted over.", shortName="I") public File INPUT
    • OUTPUT

      @Argument(doc="Where to write lifted-over haplotype database.", shortName="O") public File OUTPUT
    • SEQUENCE_DICTIONARY

      @Argument(doc="Sequence dictionary to write into the output haplotype database. (Any file from which a dictionary is extractable.)", shortName="SD") public File SEQUENCE_DICTIONARY
    • CHAIN

      @Argument(doc="Chain file that guides LiftOver. (UCSC format)") public File CHAIN
    • LIFTOVER_FAILED_FOR_ONE_OR_MORE_SNPS

      public static final int LIFTOVER_FAILED_FOR_ONE_OR_MORE_SNPS
      See Also:
  • Constructor Details

    • LiftOverHaplotypeMap

      public LiftOverHaplotypeMap()
  • 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.