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, 13:45, 13 July 2011
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| Scaled mutation rate : --theta [1.0e-03] | | Scaled mutation rate : --theta [1.0e-03] |
| Prior of ts/tv ratio : --tstv [2.00] | | Prior of ts/tv ratio : --tstv [2.00] |
− | de novo mutation : --denovo, --denovo_rate [0.00], | + | de novo mutation : --denovo, --rate_denovo [0.00], |
− | --denovo_tstv [2.00], --denovo_min_LLR [1.00] | + | --tstv_denovo [2.00], --minLLR_denovo [1.00] |
| Optimization precision : --prec [1.0e-04] | | Optimization precision : --prec [1.0e-04] |
| Multiple threading : --nthreads [4] | | Multiple threading : --nthreads [4] |
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| --nthreads : number of threads to run and it is recommended to use 4 threads for small number of input files [''Default: 1'] | | --nthreads : number of threads to run and it is recommended to use 4 threads for small number of input files [''Default: 1'] |
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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 | + | --denovo : 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. [''Default: 1.5e-08''] | | --rate_denovo : mutation rate per haplotype per generation. [''Default: 1.5e-08''] |
| --tstv_denovo : the prior ts/tv ratio of ''de novo'' mutations. [''Default: 2.0''] | | --tstv_denovo : the prior ts/tv ratio of ''de novo'' mutations. [''Default: 2.0''] |
− | --min_denovo_LLR : minimum value of log10 likelihood ratio of allowing vs. disallowing ''de novo'' mutations in the data to output [''Default: 1.0''] | + | --minLLR_denovo : minimum value of log10 likelihood ratio of allowing vs. disallowing ''de novo'' mutations in the data to output [''Default: 1.0''] |
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| == Output files == | | == Output files == |