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, 18:33, 18 June 2011
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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. [''Default: 1e-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''] | | --min_denovo_LLR : minimum value of log10 likelihood ratio of allowing vs. disallowing ''de novo'' mutations in the data to output [''Default: 1.0''] |