Changes

Explanation of Options

Explanation of Options

        --shotgun:     Standard    [http://www.1000genomes.org/node/101 VCF file 4.0]         

            --shotgun:     Standard    [http://www.1000genomes.org/node/101 VCF file 4.0]         

        --pedfile:             Pedigree file in [http://www.sph.umich.edu/csg/abecasis/Merlin/tour/input_files.html MERLIN format]

              --pedfile:     Pedigree file in [http://www.sph.umich.edu/csg/abecasis/Merlin/tour/input_files.html MERLIN format]

        --seed:                 Seed for sampling, default 123456

                  --seed:     Seed for sampling, default 123456

        --burnin:             The number of rounds ignored at the beginning in MCMC step

              --burnin:     The number of rounds ignored at the beginning in MCMC step

        --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

        --prefix:               The prefix of output file   

              --prefix:       The prefix of output file   

        --interimInterval:   The number of rounds for interim outputs

  --interimInterval:       The number of rounds for interim outputs