View source for BamUtil: splitChromosome

[[Category:BamUtil|splitChromosome]]
[[Category:BAM Software]]
[[Category:Software]]

= Overview of the <code>splitChromosome</code> function of <code>bamUtil</code> =
The <code>splitChromosome</code> option on the [[bamUtil]] executable splits an indexed BAM file into multiple files based on the Chromosome (Reference Name).  

The files all have the same base name, but with the chromosome name ".bam" or ".sam" appended.

= Usage =

 ./bam splitChromosome --in <inputFilename>  --out <outputFileBaseName> [--noeof] [--bamout|--samout] [--params]

= Parameters =
<pre>
    Required Parameters:
        --in       : the BAM file to be split
        --out      : the base filename for the SAM/BAM files to write into.  Does not include the extension.
                     CHROM.bam or CHROM.sam will be appended to the basename where CHROM is the chromosome name.
    Optional Parameters:
        --noeof  : do not expect an EOF block on a bam file.
        --bamout : write the output files in BAM format (default).
        --samout : write the output files in SAM format.
        --params : print the parameter settings
</pre>
{{PhoneHomeParamDesc}}

== Required Parameters ==
{{InBAMInputFile}}

=== Output File Basename (<code>--out</code>) ===
Use <code>--out</code> followed by the base output filename (no extension) to specify the SAM/BAM basename to use for the output files.

The chromosome name and the appropriate extension (sam/bam) will be appended to the specified basename.

== Optional Parameters ==
{{noeofBGZFParameter}}

=== Output a BAM File (<code>--bamout</code>) ===
<code>--bamout</code> indicates to output a BAM file.  This flag is enabled by default.  

=== Output a SAM File (<code>--samout</code>) ===
Use <code>--samout</code> to output a SAM file.

{{paramsParameter}}
{{PhoneHomeParameters}}

= Return Value =
*     0: all records are successfully read and written.
* non-0: at least one record was not successfully read or written.

= Example Output =
<pre>
Reference Name: 1 has 5 records
Reference Name: 2 has 2 records
Reference Name: 3 has 1 records
Reference Name: * has 2 records
Number of records = 10
Returning: 0 (SUCCESS)
</pre>