BamUtil: splitBam - Revision history

Mktrost at 22:28, 3 January 2014

2014-01-03T22:28:52Z

← Older revision		Revision as of 22:28, 3 January 2014
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	{{PhoneHomeParameters}}		{{PhoneHomeParameters}}

			= Return Value =
			* 0: Success.
			* non-0: Failure.

	[[Category:BamUtil\|splitBam]]		[[Category:BamUtil\|splitBam]]
	[[Category:BAM Software]]		[[Category:BAM Software]]
	[[Category:Software]]		[[Category:Software]]

Mktrost at 22:15, 3 January 2014

2014-01-03T22:15:20Z

@@ Line 8: / Line 8: @@
 = Usage =
 <pre>
- Usage : ./bam splitBam [-v] -i <inputBAMFile> -o <outPrefix> [-L logFile]
+Required arguments:
 </pre>
 [[Category:BamUtil|splitBam]]
 [[Category:BAM Software]]
 [[Category:Software]]

Mktrost at 15:42, 3 April 2012

2012-04-03T15:42:57Z

← Older revision		Revision as of 15:42, 3 April 2012
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	</pre>		</pre>

	[[Category:BamUtil\|~~splitChromosome~~]]		[[Category:BamUtil\|splitBam]]
	[[Category:BAM Software]]		[[Category:BAM Software]]
	[[Category:Software]]		[[Category:Software]]

Mktrost at 17:53, 12 March 2012

2012-03-12T17:53:32Z

← Older revision		Revision as of 17:53, 12 March 2012
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	<pre>		<pre>
	Usage : ./bam ~~splitBAM~~ [-v] -i <inputBAMFile> -o <outPrefix> [-L logFile]		Usage : ./bam splitBam [-v] -i <inputBAMFile> -o <outPrefix> [-L logFile]
	</pre>		</pre>

Mktrost: moved SplitBam to BamUtil: splitBam: Now part of BamUtil

2012-01-16T21:47:18Z

moved SplitBam to BamUtil: splitBam: Now part of BamUtil

← Older revision	Revision as of 21:47, 16 January 2012
(No difference)

Mktrost: Add SplitBam to Bamutil

2012-01-16T21:44:54Z

Add SplitBam to Bamutil

← Older revision		Revision as of 21:44, 16 January 2012
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	=~~= SplitBam =~~=		= Overview of the <code>splitBam</code> function of <code>bamUtil</code> =
	~~Split~~ a BAM file into multiple BAM files based on ReadGroup according to the following details.		The <code>splitBam</code> option on the [[bamUtil]] executable split a BAM file into multiple BAM files based on ReadGroup according to the following details.
	# Creates multiple output files named [outprefix].[RGID].bam, for each ReadGroup ID (RGID) existing in the bam file		# Creates multiple output files named [outprefix].[RGID].bam, for each ReadGroup ID (RGID) existing in the bam file
	# Headers are a copy of the original file, removing @RG and @PG headers where IDs match with the other ReadGroup IDs.		# Headers are a copy of the original file, removing @RG and @PG headers where IDs match with the other ReadGroup IDs.
	# Copy each of the original file's BAM record to one of the output file where the ReadGroup ID matches		# Copy each of the original file's BAM record to one of the output file where the ReadGroup ID matches


			= Usage =

	<pre>		<pre>
	Usage : splitBAM [-v] -i <inputBAMFile> -o <outPrefix> [-L logFile]		Usage : ./bam splitBAM [-v] -i <inputBAMFile> -o <outPrefix> [-L logFile]
			</pre>


			= Parameters =
	Required arguments:		Required arguments:
	-i/--in [inputBAMFile] : Original BAM file containing readGroup info		-i/--in [inputBAMFile] : Original BAM file containing readGroup info
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	</pre>		</pre>

			[[Category:BamUtil\|splitChromosome]]
			[[Category:BAM Software]]
	[[Category:Software]]		[[Category:Software]]
	~~[[Category:StatGen Download]]~~
	~~[[Category:BAM Software]]~~

Mktrost at 22:47, 1 November 2010

2010-11-01T22:47:55Z

← Older revision		Revision as of 22:47, 1 November 2010
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	# Copy each of the original file's BAM record to one of the output file where the ReadGroup ID matches		# Copy each of the original file's BAM record to one of the output file where the ReadGroup ID matches
	<pre>		<pre>
	Usage : splitBAM [-v] [-i inputBAMFile~~] [~~-o outPrefix] [-L logFile]		Usage : splitBAM [-v] -i <inputBAMFile> -o <outPrefix> [-L logFile]
	Required arguments:		Required arguments:
	-i/--in [inputBAMFile] : Original BAM file containing readGroup info		-i/--in [inputBAMFile] : Original BAM file containing readGroup info

Mktrost at 22:44, 1 November 2010

2010-11-01T22:44:26Z

← Older revision		Revision as of 22:44, 1 November 2010
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	Usage : splitBAM [-v] [-i inputBAMFile] [-o outPrefix] [-L logFile]		Usage : splitBAM [-v] [-i inputBAMFile] [-o outPrefix] [-L logFile]
	Required arguments:		Required arguments:
	-i inputBAMFile : Original BAM file containing readGroup info		-i/--in [inputBAMFile] : Original BAM file containing readGroup info
	-o ~~outprefix~~ : prefix of output bam files of [outprefix].[RGID].bam		-o/--out [outPrefix] : prefix of output bam files of [outprefix].[RGID].bam
	Optional arguments:		Optional arguments:
	-L logFile : log file name. default is listFile.log		-L/--log [logFile] : log file name. default is listFile.log
	-v : turn on verbose mode		-v/--verbose : turn on verbose mode
	</pre>		</pre>

Mktrost: Created page with '== SplitBam == Split a BAM file into multiple BAM files based on ReadGroup according to the following details. # Creates multiple output files named [outprefix].[RGID].bam, for e…'

2010-11-01T22:39:51Z

Created page with '== SplitBam == Split a BAM file into multiple BAM files based on ReadGroup according to the following details. # Creates multiple output files named [outprefix].[RGID].bam, for e…'

New page

== SplitBam ==
Split a BAM file into multiple BAM files based on ReadGroup according to the following details.
# Creates multiple output files named [outprefix].[RGID].bam, for each ReadGroup ID (RGID) existing in the bam file
# Headers are a copy of the original file, removing @RG and @PG headers where IDs match with the other ReadGroup IDs.
# Copy each of the original file's BAM record to one of the output file where the ReadGroup ID matches
<pre>
Usage : splitBAM [-v] [-i inputBAMFile] [-o outPrefix] [-L logFile]
Required arguments:
-i inputBAMFile : Original BAM file containing readGroup info
-o outprefix : prefix of output bam files of [outprefix].[RGID].bam
Optional arguments:
-L logFile : log file name. default is listFile.log
-v : turn on verbose mode
</pre>

[[Category:Software]]
[[Category:StatGen Download]]
[[Category:BAM Software]]