Walks over the input reads, printing out statistics about the read length, number of clipping events, and length of the clipping to the output stream.
This Read Filter is automatically applied to the data by the Engine before processing by ReadClippingStats.
The arguments described in the entries below can be supplied to this tool to modify its behavior. For example, the -L argument directs the GATK engine restricts processing to specific genomic intervals (this is an Engine capability and is therefore available to all GATK walkers).
This table summarizes the command-line arguments that are specific to this tool. For details, see the list further down below the table.
| Name | Type | Default value | Summary |
|---|---|---|---|
| Optional | |||
| --mappedOnly | boolean | true | when this flag is set (default), statistics will be collected on mapped reads only, while unmapped reads will be discarded |
| --out | PrintStream | stdout | An output file created by the walker. Will overwrite contents if file exists |
| --skip | int | 1 | When provided, only every skip reads are analyzed |
Arguments in this list are specific to this tool. Keep in mind that other arguments are available that are shared with other tools (e.g. command-line GATK arguments); see Inherited arguments above.
when this flag is set (default), statistics will be collected on mapped reads only, while unmapped reads will be discarded.
An output file created by the walker. Will overwrite contents if file exists.
When provided, only every skip reads are analyzed.
See also Guide Index | Technical Documentation Index | Support Forum
GATK version 2.5-2-gdb4546e built at 2013/05/01 09:32:36.
