BamUtil: mergeBam - Revision history

Mktrost at 18:06, 6 January 2014

2014-01-06T18:06:51Z

← Older revision		Revision as of 18:06, 6 January 2014
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	--verbose/-v : Turn on verbose mode		--verbose/-v : Turn on verbose mode
	</pre>		</pre>
			{{PhoneHomeParamDesc}}

	== Required Parameters==		== Required Parameters==

Mktrost at 16:47, 6 January 2014

2014-01-06T16:47:24Z

@@ Line 17: / Line 17: @@
 = Usage=
 <pre>
-./bam mergeBam [-v] [--log logFile] [--list <listFile>|--in <inputFile> --in <inputFile>] --out <outFile>
+ mergeBam [-v] [--log logFile] [--ignorePI] --list <listFile> --out <outFile>
 </pre>
@@ Line 39: / Line 39: @@
 	* (Required fields)
 Optional parameters :
 --log/-L : Log file
 --verbose/-v : Turn on verbose mode
 </pre>
 [[Category:BamUtil|mergeBam]]
 [[Category:BAM Software]]
 [[Category:Software]]

Mktrost at 03:44, 30 January 2013

2013-01-30T03:44:33Z

← Older revision		Revision as of 03:44, 30 January 2013
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	= Overview of the <code>~~rgMergeBam~~</code> function of <code>bamUtil</code> =		= Overview of the <code>mergeBam</code> function of <code>bamUtil</code> =
	The <code>~~rgMergeBam~~</code> option on the [[bamUtil]] executable merges multiple BAM files appending ReadGroup IDs.		The <code>mergeBam</code> option on the [[bamUtil]] executable merges multiple BAM files appending ReadGroup IDs if necessary.

	rgMergeBam merges multiple sorted BAM files into one BAM file like 'samtools merge' command, but merges BAM headers.		As of version 1.0.7, this program was renamed from rgMergeBam to mergeBam.
	* Checks that the ~~HD and SQ tags~~ are identical across the BAM files
	* Adds @RG headers from a tabular input file containing the fields' info		mergeBam merges multiple sorted SAM/BAM files into one BAM file like 'samtools merge' command, but merges BAM headers.
	* Adds RG:Z:[RGID] tag for each record based on the source BAM file		* Checks that the non RG header fields are identical across the BAM files
	* ~~Ensures that~~ the headers are ~~identical across~~ the ~~input files and~~ that ~~input/output BAM records~~ are ~~sorted~~		* Checks that the input SAM/BAM records are sorted
			* If --list option is used:
			** Ensures that the headers are identical across the input files
			** Adds @RG headers from a tabular input file containing the fields' info
			** Adds RG:Z:[RGID] tag for each record based on the source BAM file
			* If --in is used:
			** Merges the RG headers from the files, checking that they RG IDs are unique or if they are the same that the rest of the fields are the same


	= Usage=		= Usage=
	<pre>		<pre>
	./bam ~~rgMergeBam~~ [-v] [--log logFile] --list <listFile> --out <outFile>		./bam mergeBam [-v] [--log logFile] [--list <listFile>\|--in <inputFile> --in <inputFile>] --out <outFile>
	</pre>		</pre>

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	Required parameters :		Required parameters :
	--out/-o : Output BAM file (sorted)		--out/-o : Output BAM file (sorted)
			--in/-i : BAM file to be input, must be more than one of these options.
			cannot be used with --list/-l
	--list/-l : RGAList File. Tab-delimited list consisting of following columns (with headers):		--list/-l : RGAList File. Tab-delimited list consisting of following columns (with headers):
	BAM* : Input BAM file name to be merged		BAM* : Input BAM file name to be merged
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	</pre>		</pre>

	[[Category:BamUtil\|~~rgMergeBam~~]]		[[Category:BamUtil\|mergeBam]]
	[[Category:BAM Software]]		[[Category:BAM Software]]
	[[Category:Software]]		[[Category:Software]]

Mktrost: moved BamUtil: rgMergeBam to BamUtil: mergeBam

2013-01-30T01:34:41Z

moved BamUtil: rgMergeBam to BamUtil: mergeBam

← Older revision	Revision as of 01:34, 30 January 2013
(No difference)

Mktrost: moved RGMergeBam to BamUtil: rgMergeBam

2012-04-03T18:51:48Z

moved RGMergeBam to BamUtil: rgMergeBam

← Older revision	Revision as of 18:51, 3 April 2012
(No difference)

Mktrost at 18:51, 3 April 2012

2012-04-03T18:51:33Z

← Older revision		Revision as of 18:51, 3 April 2012
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	== ~~RGMergeBAM : Merge~~ multiple BAM files appending ReadGroup IDs==		= Overview of the <code>rgMergeBam</code> function of <code>bamUtil</code> =
			The <code>rgMergeBam</code> option on the [[bamUtil]] executable merges multiple BAM files appending ReadGroup IDs.

	rgMergeBam merges multiple sorted BAM files into one BAM file like 'samtools merge' command, but merges BAM headers.		rgMergeBam merges multiple sorted BAM files into one BAM file like 'samtools merge' command, but merges BAM headers.
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	=== Usage===		= Usage=
	<pre>		<pre>
	rgMergeBam [-v] [--log logFile] --list <listFile> --out <outFile>		./bam rgMergeBam [-v] [--log logFile] --list <listFile> --out <outFile>
			</pre>

			=Parameters=
			<pre>
	Required parameters :		Required parameters :
	--out/-o : Output BAM file (sorted)		--out/-o : Output BAM file (sorted)
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	</pre>		</pre>

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

Mktrost at 22:37, 1 November 2010

2010-11-01T22:37:07Z

← Older revision		Revision as of 22:37, 1 November 2010
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	--verbose/-v : Turn on verbose mode		--verbose/-v : Turn on verbose mode
	</pre>		</pre>

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

Mktrost at 22:31, 1 November 2010

2010-11-01T22:31:31Z

← Older revision		Revision as of 22:31, 1 November 2010
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	=== Usage===		=== Usage===
	<pre>		<pre>
	rgMergeBam [-v] [--log logFile] --list listFile --out outFile		rgMergeBam [-v] [--log logFile] --list <listFile> --out <outFile>

	Required parameters :		Required parameters :

Mktrost at 22:30, 1 November 2010

2010-11-01T22:30:34Z

← Older revision		Revision as of 22:30, 1 November 2010
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	=== Usage===		=== Usage===
	<pre>		<pre>
	rgMergeBam [-v] [--log logFile] [--list listFile~~] [~~--out outFile]		rgMergeBam [-v] [--log logFile] --list listFile --out outFile

	Required parameters :		Required parameters :

Mktrost at 22:29, 1 November 2010

2010-11-01T22:29:47Z

← Older revision		Revision as of 22:29, 1 November 2010
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	=== Usage===		=== Usage===
	<pre>		<pre>
	rgMergeBam [-v] [-L logFile] [-l listFile] [-o outFile]		rgMergeBam [-v] [--log logFile] [--list listFile] [--out outFile]

	Required parameters :		Required parameters :