Splits reads that contain Ns in their cigar string (e.g.
This Read Filter is automatically applied to the data by the Engine before processing by SplitNCigarReads.
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||Write output to this BAM filename instead of STDOUT|
||false||do not have the walker hard-clip overhanging sections of the reads|
|40||max number of bases allowed in the overhang|
|1||max number of mismatches allowed in the overhang|
|150000||max reads allowed to be kept in memory at a time by the BAM writer|
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.
do not have the walker hard-clip overhanging sections of the reads
max number of bases allowed in the overhang
If there are more than this many bases in the overhang, we won't try to hard-clip them out
int 40 [ [ -? ? ] ]
max number of mismatches allowed in the overhang
If there are more than this many mismatches within the overhang regions, the whole overhang will get hard-clipped out. It is still possible in some cases that the overhang could get clipped if the number of mismatches do not exceed this value, e.g. if most of the overhang mismatches.
int 1 [ [ -? ? ] ]
max reads allowed to be kept in memory at a time by the BAM writer
For expert users only! To minimize memory consumption you can lower this number, but then the tool may skip overhang fixing in regions with too much coverage. Just make sure to give Java enough memory! 4Gb should be enough with the default value.
int 150000 [ [ -? ? ] ]
Write output to this BAM filename instead of STDOUT
GATK version 3.2-2-gec30cee built at 2014/07/17 17:54:48. GTD: NA