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--shotgun Standard VCF 4.0 file LINK
--shotgun Standard VCF 4.0 file LINK
--pedfile Pedigree file in MERLIN format LINK
--pedfile Pedigree file in MERLIN format LINK
--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
--refPhased The initial haplotypes are built on reference alleles from VCF file
--interimInterval The number of rounds for interim outputs
--interimInterval The number of rounds for interim outputs
