Filter out reads that exceed a given insert size
This filter is intended to ensure that only reads that are likely to be mapped in the right place, and therefore to be informative, will be used in analysis.
java -jar GenomeAnalysisTk.jar \ -T ToolName \ -R reference.fasta \ -I input.bam \ -o output.file \ -rf MaxInsertSize \ -maxInsert 10000
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|
|1000000||Insert size cutoff|
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.
Insert size cutoff
int 1000000 [ [ -∞ ∞ ] ]
GATK version 3.6-0-g89b7209 built at 2017/02/09 12:52:48.