Documentation

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.

Downsampling settings

This tool does not apply any downsampling by default.


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).

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
--bam_compression
 -compress
5 Compression level to use for writing BAM files
--outputRoot
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

Compression level to use for writing BAM files

Integer  5  [ [ -?  ? ] ]


--outputRoot

output BAM file

String


See also Guide Index | Tool Documentation Index | Support Forum

GATK version 3.1-1-g07a4bf8 built at 2014/03/18 07:00:36. GTD: NA