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, 18:29, 18 June 2011
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| Some of command line options are explained below and others are self-explanatory. | | Some of command line options are explained below and others are self-explanatory. |
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− | -c : minimum cutoff of posterior probability to output a variant | + | -c : minimum cutoff of posterior probability to output a variant [Default: 0.5] |
− | --theta : scaled mutation rate per site | + | --theta : scaled mutation rate per site [Default: 0.001] |
− | --tstv: prior of ts:tv ratio. Default is 2.0 | + | --tstv: prior of ts:tv ratio [Default: 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 [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 | | --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. [Default: 1e-08] |
− | --tstv_denovo : the prior ts/tv ratio of ''de novo'' mutations. Default is 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 | + | --min_denovo_LLR : minimum value of log10 likelihood ratio of allowing vs. disallowing ''de novo'' mutations in the data to output [Default: 1] |
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| == Output files == | | == Output files == |