Filter out reads based on strand orientation
This filter is useful for isolating reads from only forward or reverse strands. By default, it filters out reads from the negative (reverse) strand. This logic can be reversed by using the -filterPositive flag.
java -jar GenomeAnalysisTk.jar \ -T ToolName \ -R reference.fasta \ -I input.bam \ -o output.file \ -rf ReadStrand \ -filterPositive
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|
|false||Discard reads on the forward strand|
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 on the forward strand
GATK version 3.8-0-ge9d806836 built at 2017/07/29 01:40:22.