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

FlagArgumentsRequiredDescription
(-o|--output)outputnoThe name of the output file to write the coverage stats to. – indicates standard out. Default value: –
(-a|--annotation)annotation-basenameyesThe basename that contains the count archive for the captured target.
n/ainputyesThe basenames of the input alignments. This mode will use the .header and .count files for each alignment.
(-t|--num-threads)num-threadsnoThe number of threads to run with. When -1 defaults to the number of cores on the machine. Default value: -1
(-d|--depths)depthsnoDepth of coverage to consider when estimating percent-capture-sites-at-depth. Default value: 5,10,15,20,30
(-p|--percentiles)percentilesnoPercentiles to consider when estimating depth-captured. Comma delimited list of numbers, in the range [0-100]. Default value: 90,75,50,10,1