SplitSamFile

Divides the input data set into separate BAM files, one for each sample in the input data set.

Category Sequence Data Processing Tools

Traversal ReadWalker

PartitionBy READ

Overview

The split files are named concatenating the sample name to the end of the provided outputRoot command-line argument.

Additional Information

Read filters

This Read Filter is automatically applied to the data by the Engine before processing by SplitSamFile.

MalformedReadFilter

Command-line Arguments

Inherited arguments

The arguments described in the entries below can be supplied to this tool to modify its behavior. For example, the -L argument directs the GATK engine restricts processing to specific genomic intervals (this is an Engine capability and is therefore available to all GATK walkers).

CommandLineGATK

SplitSamFile specific arguments

This table summarizes the command-line arguments that are specific to this tool. For details, see the list further down below the table.

Name	Type	Default value	Summary
Optional
--bam_compression	Integer	5	Compression level to use for writing BAM files
--outputRoot	String	NA	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.

--bam_compression / -compress ( Integer with default value 5 )

Compression level to use for writing BAM files.

--outputRoot ( String )

output BAM file.

GATK version 2.5-2-gdb4546e built at 2013/05/01 09:32:36.