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--randomPhase: The initial haplotypes are inferred from the single marker
--randomPhase: The initial haplotypes are inferred from the single marker
--inputPhased: The initial haplotypes are directly from input VCF file
--inputPhased: The initial haplotypes are directly from input VCF file
--refPhased: The initial haplotypes are built on reference alleles from VCF file
--prefix: The prefix of output file
--interimInterval: The number of rounds for interim outputs
