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Target snps (from the pre-phasing step)
Target snps (from the pre-phasing step)
--rounds R
--rounds R
how many iterations should be run to estimate the model parameters: (i) error rate for each marker (*.erate) and (ii) crossover rates (*.rec) for each interval.
how many rounds should be run to optimize the model parameters: (i) error rate for each marker (*.erate) and (ii) crossover rates (*.rec) for each interval.
--states S
how many haplotypes to use for parameter optimization
--em
use an e-m algorithm, instead of mcmc, for parameter optimization
--rec file.rec
--rec file.rec
use crossover rates from this file
use crossover rates from this file
