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.
The following options are available in this mode
|output||no||The name of the output file to write the coverage stats to. – indicates standard out. Default value: –|
|annotation-basename||yes||The basename that contains the count archive for the captured target.|
|input||yes||The basenames of the input alignments. This mode will use the .header and .count files for each alignment.|
|num-threads||no||The number of threads to run with. When -1 defaults to the number of cores on the machine. Default value: -1|
|depths||no||Depth of coverage to consider when estimating percent-capture-sites-at-depth. Default value: 5,10,15,20,30|
|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|