This mode is used to calculate various coverage statistics for a capture experiment. It is implemented by edu.cornell.med.icb.goby.modes.CoverageMode.java.
Mode Parameters
The following options are available in this mode
| Flag | Arguments | Required | Description |
|---|---|---|---|
(-o|--output) | output | no | The name of the output file to write the coverage stats to. – indicates standard out. Default value: - |
(-a|--annotation) | annotation-basename | yes | The basename that contains the count archive for the captured target. |
n/a | input | yes | The basenames of the input alignments. This mode will use the .header and .count files for each alignment. |
(-t|--num-threads) | num-threads | no | The number of threads to run with. When -1 defaults to the number of cores on the machine. Default value: -1 |
(-d|--depths) | depths | no | Depth of coverage to consider when estimating percent-capture-sites-at-depth. Default value: 5,10,15,20,30 |
(-p|--percentiles) | percentiles | no | Percentiles to consider when estimating depth-captured. Comma delimited list of numbers, in the range [0-100]. Default value: 90,75,50,10,1 |
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