Showing docs for version 3.6-0 | The latest version is


Split a BAM file by sample

Category Sequence Data Processing Tools

Traversal ReadWalker

PartitionBy READ


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.

Usage example

 java -jar GenomeAnalysisTK.jar \
   -T SplitSamFile \
   -R reference.fasta \
   -I input.bam \
   --outputRoot myproject_

Additional Information

Read filters

These Read Filters are automatically applied to the data by the Engine before processing by SplitSamFile.

Downsampling settings

This tool does not apply any downsampling by default.

Command-line Arguments

Engine arguments

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.

SplitSamFile specific arguments

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
"" output BAM file

Argument details

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.

--outputRoot / NA

output BAM file

String  ""

Return to top

See also GATK Documentation Index | Tool Docs Index | Support Forum

GATK version 3.6-0-g89b7209 built at 2017/02/09 12:52:48.