Only use reads belonging to a specific sample
This filter is useful for isolating data from one particular sample in a multisample file.
java -jar GenomeAnalysisTk.jar \ -T ToolName \ -R reference.fasta \ -I input.bam \ -o output.file \ -rf Sample \ -goodSM NA12878
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|
|NA||The name of the sample(s) to keep, filtering out all others|
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.
The name of the sample(s) to keep, filtering out all others
R Set NA
GATK version 3.8-0-ge9d806836 built at 2017/07/29 01:40:22.