Read clipping statistics for all reads.
This Read Filter is automatically applied to the data by the Engine before processing by ReadClippingStats.
This tool does not apply any downsampling by default.
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 more details on each argument, see the list further down below the table or click on an argument name to jump directly to that entry in the list.
|Argument name(s)||Default value||Summary|
|stdout||An output file created by the walker. Will overwrite contents if file exists|
|false||Include unmapped reads in the analysis|
||1||Do not print all reads, skip some.|
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.
Include unmapped reads in the analysis
when this flag is set (default), statistics will be collected on unmapped reads as well. The default behavior is to ignore unmapped reads."
An output file created by the walker. Will overwrite contents if file exists
Do not print all reads, skip some.
print every read whose read number is divisible by SKIP. READ_NUMBER % SKIP == 0. First read in the file has read number = 1, second is 2, third is 3, ... A value of 1 means print every read. A value of 1000 means print every 1000th read.
int 1 [ [ -? ? ] ]
GATK version 3.1-1-g07a4bf8 built at 2014/03/18 07:00:36. GTD: NA