BamUtil: splitChromosome - Revision history

Mktrost at 21:43, 3 January 2014

2014-01-03T21:43:19Z

← Older revision		Revision as of 21:43, 3 January 2014
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	{{PhoneHomeParamDesc}}		{{PhoneHomeParamDesc}}

			== Required Parameters ==
	{{InBAMInputFile}}		{{InBAMInputFile}}

	== Output File Basename (<code>--out</code>) ==		=== 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.		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.		The chromosome name and the appropriate extension (sam/bam) will be appended to the specified basename.

			== Optional Parameters ==
	{{noeofBGZFParameter}}		{{noeofBGZFParameter}}

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

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

Mktrost at 20:58, 3 January 2014

2014-01-03T20:58:51Z

← Older revision		Revision as of 20:58, 3 January 2014
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	The files all have the same base name, but with the chromosome name ".bam" or ".sam" appended.		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 =		= Parameters =
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	--params : print the parameter settings		--params : print the parameter settings
	</pre>		</pre>
			{{PhoneHomeParamDesc}}

			{{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.

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

			{{noeofBGZFParameter}}

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

	~~./bam splitChromosome~~ --in <~~inputFilename~~> ~~--out~~ <~~outputFileBaseName~~> ~~[--noeof] [--bamout\|~~--samout~~] [--params]~~		== Output a SAM File (<code>--samout</code>) ==
			Use <code>--samout</code> to output a SAM file.

			{{paramsParameter}}
			{{PhoneHomeParameters}}

	= Return Value =		= Return Value =

Mktrost: Updated to actually split all chromsomes

2012-07-16T21:07:17Z

Updated to actually split all chromsomes

← Older revision		Revision as of 21:07, 16 July 2012
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	The <code>splitChromosome</code> option on the [[bamUtil]] executable splits an indexed BAM file into multiple files based on the Chromosome (Reference Name).		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 an _# where # corresponds~~ with the ~~associated reference id from the BAM file~~.		The files all have the same base name, but with the chromosome name ".bam" or ".sam" appended.

	= Parameters =		= Parameters =
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	--in : the BAM file to be split		--in : the BAM file to be split
	--out : the base filename for the SAM/BAM files to write into. Does not include the extension.		--out : the base filename for the SAM/BAM files to write into. Does not include the extension.
	_N will be appended to the basename where ~~N indicates~~ the ~~Chromosome~~.		CHROM.bam or CHROM.sam will be appended to the basename where CHROM is the chromosome name.
	Optional Parameters:		Optional Parameters:
	--noeof : do not expect an EOF block on a bam file.		--noeof : do not expect an EOF block on a bam file.
	~~--bamIndex : the path/name of the bam index file~~
	~~(if not specified, uses the --in value + ".bai")~~
	--bamout : write the output files in BAM format (default).		--bamout : write the output files in BAM format (default).
	--samout : write the output files in SAM format.		--samout : write the output files in SAM format.
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	= Usage =		= Usage =

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


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	= Example Output =		= Example Output =
	<pre>		<pre>
	Reference ~~ID -~~1 ~~has 2 records~~		Reference Name: 1 has 5 records
	~~Reference ID 0~~ has 5 records		Reference Name: 2 has 2 records
	Reference ~~ID 1~~ has 2 records		Reference Name: 3 has 1 records
	Reference ~~ID 2~~ has 1 records		Reference Name: * has 2 records
	Reference ~~ID 3~~ has ~~0 records~~
	~~Reference ID 4 has 0 records~~
	~~Reference ID 5 has 0 records~~
	~~Reference ID 6 has 0 records~~
	~~Reference ID 7 has 0 records~~
	~~Reference ID 8 has 0 records~~
	~~Reference ID 9 has 0 records~~
	~~Reference ID 10 has 0 records~~
	~~Reference ID 11 has 0 records~~
	~~Reference ID 12 has 0 records~~
	~~Reference ID 13 has 0 records~~
	~~Reference ID 14 has 0 records~~
	~~Reference ID 15 has 0 records~~
	~~Reference ID 16 has 0 records~~
	~~Reference ID 17 has 0 records~~
	~~Reference ID 18 has 0 records~~
	~~Reference ID 19 has 0 records~~
	~~Reference ID 20 has 0 records~~
	~~Reference ID 21 has 0 records~~
	~~Reference ID 22 has 0~~ records
	Number of records = 10		Number of records = 10
	Returning: 0 (SUCCESS)		Returning: 0 (SUCCESS)
	</pre>		</pre>

Mktrost: Add splitChromosome

2011-09-02T17:32:52Z

Add splitChromosome

New page

[[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 an _# where # corresponds with the associated reference id from the BAM file.

= 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.
_N will be appended to the basename where N indicates the Chromosome.
Optional Parameters:
--noeof : do not expect an EOF block on a bam file.
--bamIndex : the path/name of the bam index file
(if not specified, uses the --in value + ".bai")
--bamout : write the output files in BAM format (default).
--samout : write the output files in SAM format.
--params : print the parameter settings
</pre>

= Usage =

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

= 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 ID -1 has 2 records
Reference ID 0 has 5 records
Reference ID 1 has 2 records
Reference ID 2 has 1 records
Reference ID 3 has 0 records
Reference ID 4 has 0 records
Reference ID 5 has 0 records
Reference ID 6 has 0 records
Reference ID 7 has 0 records
Reference ID 8 has 0 records
Reference ID 9 has 0 records
Reference ID 10 has 0 records
Reference ID 11 has 0 records
Reference ID 12 has 0 records
Reference ID 13 has 0 records
Reference ID 14 has 0 records
Reference ID 15 has 0 records
Reference ID 16 has 0 records
Reference ID 17 has 0 records
Reference ID 18 has 0 records
Reference ID 19 has 0 records
Reference ID 20 has 0 records
Reference ID 21 has 0 records
Reference ID 22 has 0 records
Number of records = 10
Returning: 0 (SUCCESS)
</pre>