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 Detail

      • 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 Detail

      • MergePedIntoVcf

        public MergePedIntoVcf()
    • 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.