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, 18:26, 18 June 2011
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| -c : minimum cutoff of posterior probability to output a variant | | -c : minimum cutoff of posterior probability to output a variant |
| --theta : scaled mutation rate per site | | --theta : scaled mutation rate per site |
| + | --tstv: prior of ts:tv ratio. Default is 2.0 |
| --nthreads : number of threads to run and it is recommended to use 4 threads for small number of input files. | | --nthreads : number of threads to run and it is recommended to use 4 threads for small number of input files. |
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| --de_novo : a boolean flag to turn on ''de novo'' mutation detection. The following options take effect only when this flag is ON | | --de_novo : a boolean flag to turn on ''de novo'' mutation detection. The following options take effect only when this flag is ON |
| --rate_denovo : mutation rate per haplotype per generation. Usually it is on the order of 1e-08 | | --rate_denovo : mutation rate per haplotype per generation. Usually it is on the order of 1e-08 |
− | --tstv_denovo : the prior ts/tv ratio of ''de novo'' mutations | + | --tstv_denovo : the prior ts/tv ratio of ''de novo'' mutations. Default is 2.0 |
| --min_denovo_LLR : minimum value of log10 likelihood ratio of allowing vs. disallowing ''de novo'' mutations in the data to output | | --min_denovo_LLR : minimum value of log10 likelihood ratio of allowing vs. disallowing ''de novo'' mutations in the data to output |
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