Filter out reads based on length
This filter is useful for running on only reads that are longer (or shorter) than the given threshold sizes.
java -jar GenomeAnalysisTk.jar \ -T ToolName \ -R reference.fasta \ -I input.bam \ -o output.file \ -rf ReadLength \ -minRead 50 \ -maxRead 101
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|
|0||Discard reads with length greater than the specified value|
|1||Discard reads with length shorter than the specified value|
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.
Discard reads with length greater than the specified value
R int 0 [ [ -∞ ∞ ] ]
Discard reads with length shorter than the specified value
R int 1 [ [ -∞ ∞ ] ]
GATK version 3.6-0-g89b7209 built at 2017/02/09 12:52:48.