Package picard.arrays

Class MergePedIntoVcf


@DocumentedFeature public class MergePedIntoVcf extends CommandLineProgram
Class to take genotype calls from a ped file output from zCall and merge them into a vcf from autocall.
  • Field Details

    • ORIGINAL_VCF

      @Argument(shortName="VCF", doc="The vcf containing the original autocall genotypes.") public File ORIGINAL_VCF
    • PED_FILE

      @Argument(shortName="PED", doc="PED file to be merged into VCF.") public File PED_FILE
    • MAP_FILE

      @Argument(shortName="MAP", doc="MAP file for the PED file.") public File MAP_FILE
    • ZCALL_THRESHOLDS_FILE

      @Argument(shortName="ZCALL_T_FILE", doc="The zcall thresholds file.") public File ZCALL_THRESHOLDS_FILE
    • ZCALL_VERSION

      @Argument(shortName="ZCALL_VERSION", doc="The version of zcall used") public String ZCALL_VERSION
    • OUTPUT

      @Argument(shortName="O", doc="The output VCF file to write with merged genotype calls.") public File OUTPUT
  • Constructor Details

    • MergePedIntoVcf

      public MergePedIntoVcf()
  • 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.