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, 16:47, 11 February 2012
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| --minLLR_denovo : 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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− | --chr2process: the chromosome names to process. If multiple chromosomes are provided, they should be separated by comma, e.g. --chr2process 2,10 or --chr2process chr2,chr10 | + | --chr2process: the chromosome names to process. Default is empty and is to process all chromosomes in the input. |
| + | If multiple chromosomes are provided, they should be separated by comma, e.g. --chr2process 2,10 or --chr2process chr2,chr10 |
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| --gl_off: not to output genotype likelihood values for each individual. Default is to output 3 GLs for polymorphisms and 10 GLs for de novo mutations | | --gl_off: not to output genotype likelihood values for each individual. Default is to output 3 GLs for polymorphisms and 10 GLs for de novo mutations |