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Available Options
Available Options
Shotgun Sequences : --shotgun [], --pedfile []
Shotgun Sequences : --shotgun [], --pedfile []
Markov Sampler : --seed [], --burnin, --rounds []
Markov Sampler : --seed [], --burnin [], --rounds []
Haplotyper : --states, --errorRate [], --compact
Haplotyper : --states [], --compact
Phasing : --randomPhase [], --inputPhased, --refPhased
Phasing : --randomPhase , --inputPhased, --refPhased
Output Files : --prefix [], --phase, --interimInterval []
Output Files : --prefix [], --phase [], --interimInterval
Explanation of Options
Explanation of Options
--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]
--shotgun: Standard [http://www.1000genomes.org/node/101 VCF file 4.0]
--randomPhase The initial haplotypes are inferred from the single marker
--pedfile: Pedigree file in [http://www.sph.umich.edu/csg/abecasis/Merlin/tour/input_files.html MERLIN format]
--inputPhased The initial haplotypes are directly from input VCF file
--seed: Seed for sampling, default 123456
--refPhased The initial haplotypes are built on reference alleles from VCF file
--burnin: The number of rounds ignored at the beginning in MCMC step
--interimInterval The number of rounds for interim outputs
--randomPhase: The initial haplotypes are inferred from the single marker
--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
