BamUtil: bam2FastQ - Revision history

Mktrost: /* Parameters */

2016-03-06T03:53:50Z

Parameters

← Older revision		Revision as of 03:53, 6 March 2016
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	= Parameters =		= Parameters =
	<pre>		<pre>
	Required Parameters:		Required Parameters:
	--in : the SAM/BAM file to convert to FastQ		--in : the SAM/BAM file to convert to FastQ
	Optional Parameters:		Optional Parameters:
	--readname : Process the BAM as readName sorted instead		--readname : Process the BAM as readName sorted instead
	of coordinate if the header does not indicate a sort order.		of coordinate if the header does not indicate a sort order.
	--merge : Generate 1 interleaved (merged) FASTQ for paired-ends (unpaired in a separate file)		--splitRG : Split into RG specific fastqs.
	use firstOut to override the filename of the interleaved file.		--qualField : Use the base quality from the specified tag
	--refFile : Reference file for converting '=' in the sequence to the actual base		rather than from the Quality field (default)
	if '=' are found and the refFile is not specified, 'N' is written to the FASTQ		--merge : Generate 1 interleaved (merged) FASTQ for paired-ends (unpaired in a separate file)
	--firstRNExt : read name extension to use for first read in a pair		use firstOut to override the filename of the interleaved file.
	default is "/1"		--refFile : Reference file for converting '=' in the sequence to the actual base
	--secondRNExt : read name extension to use for second read in a pair		if '=' are found and the refFile is not specified, 'N' is written to the FASTQ
	default is "/2"		--firstRNExt : read name extension to use for first read in a pair
	--rnPlus : Add the Read Name/extension to the '+' line of the fastq records		default is "/1"
	--noReverseComp : Do not reverse complement reads marked as reverse		--secondRNExt : read name extension to use for second read in a pair
	--noeof : Do not expect an EOF block on a bam file.		default is "/2"
	--params : Print the parameter settings to stderr		--rnPlus : Add the Read Name/extension to the '+' line of the fastq records
	Optional OutputFile Names:		--noReverseComp : Do not reverse complement reads marked as reverse
	--outBase : Base output name for generated output files		--region : Only convert reads containing the specified region/nucleotide.
	--firstOut : Output name for the first in pair file		Position formatted as: chr:pos:base
	over-rides setting of outBase		pos (0-based) & base are optional.
	--secondOut : Output name for the second in pair file		--gzip : Compress the output FASTQ files using gzip
	over-rides setting of outBase		--noeof : Do not expect an EOF block on a bam file.
	--unpairedOut : Output name for unpaired reads		--params : Print the parameter settings to stderr
	over-rides setting of outBase		Optional OutputFile Names:
			--outBase : Base output name for generated output files
			--firstOut : Output name for the first in pair file
			over-rides setting of outBase
			--secondOut : Output name for the second in pair file
			over-rides setting of outBase
			--unpairedOut : Output name for unpaired reads
			over-rides setting of outBase
	</pre>		</pre>

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	The file does not need to be strictly sorted by read name. The only requirement is that matching read names are next to each other.		The file does not need to be strictly sorted by read name. The only requirement is that matching read names are next to each other.

			=== Split into RG Specific FASTQs (<code>--splitRG</code>) ===

			Create RG specific FASTQ files.

			Cannot be specified with firstOut/secondOut/unpairedOut since there will be a different filename for each RG.

			Cannot write to stdout when <code>--splitRG</code> is specified.

			Output filenames will be <outBase>.<RG>_1.fastq, <outBase>.<RG>_2.fastq, and <outBase>.<RG>.fastq. A fastq list file <outBase>.list will be created containing MERGE_NAME (the RG tag's SM value or outBase if the value is empty), fastq 1, fastq 2 (or . if it is a single ended fastq), and the RG tag string.

			=== Use the Base Quality from the Specified Tag (<code>--qualField</code>) ===

			By default, the quality field is used for the Base Qualities in the FASTQ file. Specify <code>--qualField <tagName></code> to use the base qualities from the specified tag instead of the quality field.


	=== Generate 1 Paired-End Output File (<code>--merge</code>) ===		=== Generate 1 Paired-End Output File (<code>--merge</code>) ===
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	Specifying <code>--noReverseComp</code> would result in a FASTQ sequence of ACCGTG		Specifying <code>--noReverseComp</code> would result in a FASTQ sequence of ACCGTG

			=== Only Convert the Specified Region (<code>--region</code>) ===

			Only convert reads containing the specified region/nucleotide.

			Position formatted as: chr:pos:base

			pos (0-based) & base are optional.

	{{noeofBGZFParameter}}		{{noeofBGZFParameter}}

Mktrost: /* Usage */

2016-03-06T03:36:19Z

Usage

← Older revision		Revision as of 03:36, 6 March 2016
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	= Usage =		= Usage =
	./bam bam2FastQ --in <inputFile> [--readName] [--refFile <referenceFile>] [--outBase <outputFileBase>] [--firstOut <1stReadInPairOutFile>] [--merge\|--secondOut <2ndReadInPairOutFile>] [--unpairedOut <unpairedOutFile>] [--firstRNExt <~~firstInPairReadNameExt~~>] [--secondRNExt <secondInPairReadNameExt>] [--rnPlus] [--noReverseComp] [--noeof] [--params]		./bam bam2FastQ --in <inputFile> [--readName] [--splitRG] [--qualField <tag>] [--refFile <referenceFile>] [--outBase <outputFileBase>] [--firstOut <1stReadInPairOutFile>] [--merge\|--secondOut <2ndReadInPairOutFile>] [--unpairedOut <unpairedOutFile>] [--firstRNExt <firstInPairReadNameEx t>] [--secondRNExt <secondInPairReadNameExt>] [--rnPlus] [--noReverseComp] [--region <chr>[:<pos>[:<base>]]] [--gzip] [--noeof] [--params]

	= Parameters =		= Parameters =

Mktrost: /* Overview of the bam2FastQ function of bamUtil */

2016-03-06T03:35:04Z

Overview of the bam2FastQ function of bamUtil

← Older revision		Revision as of 03:35, 6 March 2016
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	The <code>bam2FastQ</code> option on the [[bamUtil]] converts a BAM file into FastQ files. This is necessary when only BAM files are delivered but a new alignment is desired. By converting BAM to FastQ files new alignments can be done using FastQ files		The <code>bam2FastQ</code> option on the [[bamUtil]] converts a BAM file into FastQ files. This is necessary when only BAM files are delivered but a new alignment is desired. By converting BAM to FastQ files new alignments can be done using FastQ files

	'''NOTE: ~~This tool does not work on templates that have more than 2 segments~~. It ~~does not properly match~~ reads ~~when more than~~ 2 ~~reads have~~ the same read name.'''		'''NOTE: Secondary and Supplementary reads are skipped when converting to FastQ. It assumes that there will only be 2 reads (the 2 primary mates) with the same read name that are not secondary or supplementary.'''

	'''NOTE: ~~This tool does not~~ split reads into read group specific FASTQs~~. If you want Read Group specific FASTQ files, first run [[BamUtil: splitBam]] to first split the BAM into 1 BAM per Read Group. Then run bam2FastQ on each bam~~.'''		'''NOTE: Use the --splitRG option to split reads into read group specific FASTQs.'''

	== How to use it ==		== How to use it ==

Mktrost at 16:26, 30 October 2014

2014-10-30T16:26:03Z

← Older revision		Revision as of 16:26, 30 October 2014
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	The <code>bam2FastQ</code> option on the [[bamUtil]] converts a BAM file into FastQ files. This is necessary when only BAM files are delivered but a new alignment is desired. By converting BAM to FastQ files new alignments can be done using FastQ files		The <code>bam2FastQ</code> option on the [[bamUtil]] converts a BAM file into FastQ files. This is necessary when only BAM files are delivered but a new alignment is desired. By converting BAM to FastQ files new alignments can be done using FastQ files

	NOTE: This tool does not work on templates that have more than 2 segments. It does not properly match reads when more than 2 reads have the same read name.		'''NOTE: This tool does not work on templates that have more than 2 segments. It does not properly match reads when more than 2 reads have the same read name.'''

			'''NOTE: This tool does not split reads into read group specific FASTQs. If you want Read Group specific FASTQ files, first run [[BamUtil: splitBam]] to first split the BAM into 1 BAM per Read Group. Then run bam2FastQ on each bam.'''

	== How to use it ==		== How to use it ==
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	Any errors and a summary of how many pairs and unpaired reads were processed are written to stderr.		Any errors and a summary of how many pairs and unpaired reads were processed are written to stderr.

	NOTE: This tool does not work on templates that have more than 2 segments. It does not properly match reads when more than 2 reads have the same read name.		'''NOTE: This tool does not work on templates that have more than 2 segments. It does not properly match reads when more than 2 reads have the same read name.'''

			'''NOTE: This tool does not split reads into read group specific FASTQs. If you want Read Group specific FASTQ files, first run [[BamUtil: splitBam]] to first split the BAM into 1 BAM per Read Group. Then run bam2FastQ on each bam.'''

	=== Output Files ===		=== Output Files ===

Mktrost: /* Output Files */

2014-01-06T22:48:20Z

Output Files

← Older revision		Revision as of 22:48, 6 January 2014
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	You can optionally directly specify the output fastq filenames using:		You can optionally directly specify the output fastq filenames using:
	* --firstOut firstReadInAPair.fastq (also used for the interleaved filename with [[#Generate 1 Paired-End Output File (--merge)\|<code>--merge</code>]].		* --firstOut firstReadInAPair.fastq (also used for the interleaved filename with [[#Generate 1 Paired-End Output File (--merge)\|<code>--merge</code>]])
	* --secondOut secondReadInAPair.fastq		* --secondOut secondReadInAPair.fastq
	* --unpairedOut unpairedReads.fastq		* --unpairedOut unpairedReads.fastq

Mktrost at 22:47, 6 January 2014

2014-01-06T22:47:38Z

Show changes

Mktrost at 15:35, 18 May 2012

2012-05-18T15:35:53Z

← Older revision		Revision as of 15:35, 18 May 2012
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	= Overview of the <code>bam2FastQ</code> function of <code>[[bamUtil]]</code> =		= Overview of the <code>bam2FastQ</code> function of <code>[[bamUtil]]</code> =
	The <code>bam2FastQ</code> option on the [[bamUtil]] converts a BAM file into FastQ files. This is necessary when only BAM files are delivered but a new alignment is desired. By converting BAM to FastQ files new alignments can be done using FastQ files		The <code>bam2FastQ</code> option on the [[bamUtil]] converts a BAM file into FastQ files. This is necessary when only BAM files are delivered but a new alignment is desired. By converting BAM to FastQ files new alignments can be done using FastQ files

			NOTE: This tool does not work on templates that have more than 2 segments. It does not properly match reads when more than 2 reads have the same read name.


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	Any errors and a summary of how many pairs and unpaired reads were processed are written to stderr.		Any errors and a summary of how many pairs and unpaired reads were processed are written to stderr.

			NOTE: This tool does not work on templates that have more than 2 segments. It does not properly match reads when more than 2 reads have the same read name.

	=== Output Files ===		=== Output Files ===

Mktrost: /* Usage */

2012-05-17T21:26:09Z

Usage

← Older revision		Revision as of 21:26, 17 May 2012
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	= Usage =		= Usage =
	./bam bam2FastQ --in <inputFile> [--readName] [--refFile <referenceFile>] [--outBase <outputFileBase>] [--firstOut <1stReadInPairOutFile>] [--secondOut <2ndReadInPairOutFile>] [--unpairedOut <unpairedOutFile>] [--firstRNExt <firstInPairReadNameExt>] [--secondRNExt <secondInPairReadNameExt>] [--rnPlus] [--noReverseComp] [--noeof] [--params]		./bam bam2FastQ --in <inputFile> [--readName] [--refFile <referenceFile>] [--outBase <outputFileBase>] [--firstOut <1stReadInPairOutFile>] [--secondOut <2ndReadInPairOutFile>] [--unpairedOut <unpairedOutFile>] [--firstRNExt <firstInPairReadNameExt>] [--secondRNExt <secondInPairReadNameExt>] [--rnPlus] [--noReverseComp] [--noeof] [--params]


	= Parameters =		= Parameters =

Mktrost at 21:25, 17 May 2012

2012-05-17T21:25:44Z

← Older revision		Revision as of 21:25, 17 May 2012
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	~~=This functionality will be released on 5/17/2012=~~

	= Overview of the <code>bam2FastQ</code> function of <code>[[bamUtil]]</code> =		= Overview of the <code>bam2FastQ</code> function of <code>[[bamUtil]]</code> =
	The <code>bam2FastQ</code> option on the [[bamUtil]] converts a BAM file into FastQ files. This is necessary when only BAM files are delivered but a new alignment is desired. By converting BAM to FastQ files new alignments can be done using FastQ files		The <code>bam2FastQ</code> option on the [[bamUtil]] converts a BAM file into FastQ files. This is necessary when only BAM files are delivered but a new alignment is desired. By converting BAM to FastQ files new alignments can be done using FastQ files
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	When processing files sorted by read name, the only requirement is that matching read names are next to each other. It does not need to be in strict alphabetical order.		When processing files sorted by read name, the only requirement is that matching read names are next to each other. It does not need to be in strict alphabetical order.

			Read Names in paired-end FASTQ files are appended with "/1" for the first in the pair, and "/2" for the second in the pair. Override these defaults using [[#First in Pair FastQ ReadName Extension (--firstRNExt)\|--firstRNExt]] and [[#Second in Pair FastQ ReadName Extension (--secondRNExt)\|--secondRNExt]]

			Sequences marked as Reverse strands in the SAM/BAM file are reverse complemented prior to writing to the FASTQ files. To skip this step, specify [[#Do Not Reverse Complement Reverse Strands (--noReverseComp)\|--noReverseComp]]

	Any errors and a summary of how many pairs and unpaired reads were processed are written to stderr.		Any errors and a summary of how many pairs and unpaired reads were processed are written to stderr.
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	{{inBAMInputFile}}		{{inBAMInputFile}}

			== BAM File Is Sorted By Read Name (<code>--readname</code>) ==

			The bam2FastQ program by default checks the sort order in the SAM/BAM header when converting to FASTQ, and if that is not specified, assumes it is sorted by coordinate.

			To override the default and force it to assume the file is sorted by readname, specify the <code>--readName</code> option

			The file does not need to be strictly sorted by read name. The only requirement is that matching read names are next to each other.

			== Reference File for Converting '=' in the Sequence to Bases <code>--refFile</code>==
			If the SAM/BAM file contains '=' in the sequence instead of the actual bases, the bam2FastQ program needs to convert the '=' back to the bases. To do that it needs the reference. Specify the reference by using <code>--refFile</code> followed by the reference filename.

			For example:
			./bam bam2FastQ --in myFile.bam --refFile myPath/myRefFile.fa

	== Output FastQ File Base Name (<code>--outBase</code>) ==		== Output FastQ File Base Name (<code>--outBase</code>) ==
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	The value specified by this parameter is overridden by <code>--firstOut</code>, <code>--secondOut</code>, and <code>--unpairedOut</code>, but is used for whichever output files are not specified.		The value specified by this parameter is overridden by <code>--firstOut</code>, <code>--secondOut</code>, and <code>--unpairedOut</code>, but is used for whichever output files are not specified.


	== Output FastQ File Name For the First End of Paired End (<code>--firstOut</code>) ==		== Output FastQ File Name For the First End of Paired End (<code>--firstOut</code>) ==
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	For example:		For example:
	./bam bam2FastQ --in myFile.bam --firstOut myFileEnd1.fastq		./bam bam2FastQ --in myFile.bam --firstOut myFileEnd1.fastq


	== Output FastQ File Name For the Second End of Paired End (<code>--secondOut</code>) ==		== Output FastQ File Name For the Second End of Paired End (<code>--secondOut</code>) ==
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	For example:		For example:
	./bam bam2FastQ --in myFile.bam --secondOut myFileEnd2.fastq		./bam bam2FastQ --in myFile.bam --secondOut myFileEnd2.fastq


	== Output FastQ File Name For Unpaired Reads (<code>--unpairedOut</code>) ==		== Output FastQ File Name For Unpaired Reads (<code>--unpairedOut</code>) ==
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	./bam bam2FastQ --in myFile.bam --unpairedOut myFileUnpaired.fastq		./bam bam2FastQ --in myFile.bam --unpairedOut myFileUnpaired.fastq

			== First in Pair FastQ ReadName Extension (<code>--firstRNExt</code>) ==

	== ~~BAM File Is Sorted By~~ Read Name (<code>--~~readname~~</code>) ==		<code>--firstRNExt</code> overrides the default "/1" that is appended to the Read Name of the first-end of a read pair with the specified value.

			== Second in Pair FastQ ReadName Extension (<code>--secondRNExt</code>) ==

			<code>--secondRNExt</code> overrides the default "/2" that is appended to the Read Name of the second-end of a read pair with the specified value.

			== Include the Read Name on the "+" line of the FASTQ (<code>--rnPlus</code>) ==

			By default the read name is not included on the "+" line of the FASTQ files. To include the read name and the extension for paired-end reads, specify <code>--rnPlus</code>.

			== Do Not Reverse Complement Reverse Strands (<code>--noReverseComp</code>) ==

			By default, reads marked as reverse in the BAM file are reverse complemented prior to writing to the FASTQ files. <code>--noReverseComp</code> disables this feature, and skips the reverse complement step.

			For example, if a sequence is ACCGTG marked as reverse, the default FASTQ record will be written as: CACGGT

	~~The bam2FastQ program by default checks the sort order~~ in ~~the SAM/BAM header when converting to~~ FASTQ~~, and if that is not specified, assumes it is sorted by coordinate.~~		Specifying <code>--noReverseComp</code> would result in a FASTQ sequence of ACCGTG

	~~To override the default and force it to assume the file is sorted by readname, specify the <code>--readName</code> option~~		{{noeofBGZFParameter}}
			{{paramsParameter}}

	~~The file does not need to be strictly sorted by read name. The only requirement is that matching read names are next to each other.~~

			= Return Value =

	~~== Reference File for Converting '=' in the Sequence to Bases <code>~~-~~-refFile</code>==~~		Returns -1 if input parameters are invalid.
	If the SAM/BAM file contains '=' in the sequence instead of the actual bases, the bam2FastQ program needs to convert the '=' back to the bases. To do that it needs the reference. Specify the reference by using <code>--refFile</code> followed by the reference filename.

	~~For example:~~		Returns the SamStatus for the reads/writes (0 on success).
	~~./bam bam2FastQ --in myFile.bam --refFile myPath~~/~~myRefFile~~.fa

Mktrost at 21:49, 16 May 2012

2012-05-16T21:49:40Z

← Older revision		Revision as of 21:49, 16 May 2012
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			=This functionality will be released on 5/17/2012=

	= Overview of the <code>bam2FastQ</code> function of <code>[[bamUtil]]</code> =		= Overview of the <code>bam2FastQ</code> function of <code>[[bamUtil]]</code> =
	The <code>bam2FastQ</code> option on the [[bamUtil]] converts a BAM file into FastQ files. This is necessary when only BAM files are delivered but a new alignment is desired. By converting BAM to FastQ files new alignments can be done using FastQ files		The <code>bam2FastQ</code> option on the [[bamUtil]] converts a BAM file into FastQ files. This is necessary when only BAM files are delivered but a new alignment is desired. By converting BAM to FastQ files new alignments can be done using FastQ files


	== How to use it ==		== How to use it ==