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The initial set of genotype calls is generated examining a single individual at a time. These calls are typically quite good for deep sequencing data, but much less accurate for low pass sequence data. In either case, they can be greatly improved by models that combine information across sites and individuals.
The initial set of genotype calls is generated examining a single individual at a time. These calls are typically quite good for deep sequencing data, but much less accurate for low pass sequence data. In either case, they can be greatly improved by models that combine information across sites and individuals.
The following parameters are available. Ones with "[]" are in effect:
Available Options
Shotgun Sequences : --shotgun [],
--pedfile []
Markov Sampler : --seed [123456], --burnin, --rounds [2]
Haplotyper : --states, --errorRate [0.01], --compact
Phasing : --randomPhase [ON], --inputPhased, --refPhased
Imputation : --geno, --quality, --dosage [ON], --probs
Output Files : --prefix [], --phase [ON], --interimInterval
Here is how that might work:
Here is how that might work:
