Split a BAM file by sample
This tool divides the input data set into separate BAM files, one for each sample in the input data set. The split files are named by concatenating the sample name to the end of the provided outputRoot command-line argument.
A single bam file.
A separate bam file for each sample.
java -jar GenomeAnalysisTK.jar \ -T SplitSamFile \ -R reference.fasta \ -I input.bam \ --outputRoot myproject_
These Read Filters are automatically applied to the data by the Engine before processing by SplitSamFile.
This tool does not apply any downsampling by default.
All tools inherit arguments from the GATK Engine' "CommandLineGATK" argument collection, which can be used to modify various aspects of the tool's function. For example, the -L argument directs the GATK engine to restrict processing to specific genomic intervals; or the -rf argument allows you to apply certain read filters to exclude some of the data from the analysis.
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 | |
|---|---|---|---|
| Optional Parameters | |||
| --outputRoot |
"" | output BAM file | |
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.
output BAM file
String ""