BamUtil: polishBam - Revision history

Mktrost at 18:06, 6 January 2014

2014-01-06T18:06:20Z

← Older revision		Revision as of 18:06, 6 January 2014
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	--checkSQ : check the consistency of SQ tags (SN and LN) with existing header lines. Must be used with --fasta option		--checkSQ : check the consistency of SQ tags (SN and LN) with existing header lines. Must be used with --fasta option
	</pre>		</pre>
			{{PhoneHomeParamDesc}}

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

Mktrost at 17:17, 6 January 2014

2014-01-06T17:17:49Z

@@ Line 23: / Line 23: @@
 </pre>
 = Return Value =
-Returns 0.
+Returns 0 on success, non-0 on failure.
 = Example =

Mktrost: moved PolishBam to BamUtil: polishBam

2012-04-03T18:49:30Z

moved PolishBam to BamUtil: polishBam

← Older revision	Revision as of 18:49, 3 April 2012
(No difference)

Mktrost at 18:48, 3 April 2012

2012-04-03T18:48:22Z

← Older revision		Revision as of 18:48, 3 April 2012
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	</pre>		</pre>


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

Mktrost: Update polish bam

2012-04-03T18:47:54Z

Update polish bam

← Older revision		Revision as of 18:47, 3 April 2012
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	=~~= Polish BAM =~~=		= Overview of the <code>polishBam</code> function of <code>bamUtil</code> =
	The <code>polishBam</code> ~~program is released as part of~~ the ~~StatGen Library~~ & ~~Tools download~~.		The <code>polishBam</code> option on the [[bamUtil]] executable adds/updates header lines & adds the RG tag to each record.

	<~~code~~>~~polishBam~~<~~/code~~> ~~trims the end of reads in a SAM/BAM file, changing read ends to ‘N’ and quality to ‘!’.~~		= Usage =
			./bam polishBam (options) --in <inBamFile> --out <outBamFile>

			= Parameters =
	=== Parameters ===
	<pre>		<pre>
	Required parameters:		Required parameters:
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	--checkSQ : check the consistency of SQ tags (SN and LN) with existing header lines. Must be used with --fasta option		--checkSQ : check the consistency of SQ tags (SN and LN) with existing header lines. Must be used with --fasta option
	</pre>		</pre>

	~~=== Usage ===~~
	~~polishBAM (options) --in <inBamFile> --out <outBamFile>~~


	=== Return Value ===		= Return Value =
	Returns 0.		Returns 0.

	=== Example ===		= Example =
	Command:		Command:
	<pre>		<pre>
	../~~../bin/~~polishBam --in testFiles/sortedSam.sam --out results/updatedSam.sam --log results/updated.log --checkSQ --fasta testFiles/testFasta.fa --AS my37 --UR testFasta.fa --RG "@RG ID:UM0037:1 SM:Sample2 LB:lb2 PU:mypu CN:UMCORE DT:2010-11-01 PL:ILLUMINA" --PG "@PG ID:polish VN:0.0.1" --SP new --HD "@HD VN:1.0 SO:coordinate GO:none"		./bam polishBam --in testFiles/sortedSam.sam --out results/updatedSam.sam --log results/updated.log --checkSQ --fasta testFiles/testFasta.fa --AS my37 --UR testFasta.fa --RG "@RG ID:UM0037:1 SM:Sample2 LB:lb2 PU:mypu CN:UMCORE DT:2010-11-01 PL:ILLUMINA" --PG "@PG ID:polish VN:0.0.1" --SP new --HD "@HD VN:1.0 SO:coordinate GO:none"
	</pre>		</pre>

Mktrost at 20:21, 1 November 2010

2010-11-01T20:21:32Z

@@ Line 30: / Line 30: @@
 Returns 0.
-=== Example Output ===
+=== Example ===
 <pre>
 </pre>

Mktrost at 19:21, 29 October 2010

2010-10-29T19:21:55Z

← Older revision		Revision as of 19:21, 29 October 2010
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	=== Usage ===		=== Usage ===
	polishBAM (options) --in=<inBamFile> --out=<outBamFile>		polishBAM (options) --in <inBamFile> --out <outBamFile>


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	=== Example Output ===		=== Example Output ===
	<pre>		<pre>
	~~polishBAM (options) --in=<inBamFile> --out=<outBamFile>~~
	</pre>		</pre>

Mktrost at 18:47, 29 October 2010

2010-10-29T18:47:57Z

← Older revision		Revision as of 18:47, 29 October 2010
Line 24:		Line 24:

	=== Usage ===		=== Usage ===
	~~trimBam [inFile] [outFile] [num~~-~~bases~~-to-~~trim~~-~~on-each-side]~~		polishBAM (options) --in=<inBamFile> --out=<outBamFile>


	=== Return Value ===		=== Return Value ===
	Returns ~~the SamStatus for the reads/writes.~~ 0 ~~on success~~.		Returns 0.

	=== Example Output ===		=== Example Output ===

Mktrost at 18:46, 29 October 2010

2010-10-29T18:46:31Z

← Older revision		Revision as of 18:46, 29 October 2010
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	== ~~Trim~~ BAM ==		== Polish BAM ==
	The <code>~~trimBam~~</code> program is released as part of the StatGen Library & Tools download.		The <code>polishBam</code> program is released as part of the StatGen Library & Tools download.

	<code>~~trimBam~~</code> trims the end of reads in a SAM/BAM file, changing read ends to ‘N’ and quality to ‘!’.		<code>polishBam</code> trims the end of reads in a SAM/BAM file, changing read ends to ‘N’ and quality to ‘!’.


	=== Parameters ===		=== Parameters ===
	<pre>		<pre>
	Required ~~Parameters~~:		Required parameters:
	~~inFile~~ : ~~the SAM~~/BAM file to be ~~read~~		-i/--in : input BAM file
	~~outFile~~ : ~~the SAM~~/~~BAM~~ file to ~~be written~~		-o/--out : output BAM file
	~~num~~-~~bases~~-to-~~trim~~-on-~~each~~-~~side~~ : the ~~number~~ of ~~bases/qualities to trim from each side~~		Optional parameters:
			-v : turn on verbose mode
			-l/--log : writes logfile. <outBamFile>.log will be used if value is unspecified
			--HD : add @HD header line
			--RG : add @RG header line
			--PG : add @PG header line
			-f/--fasta : fasta reference file to compute MD5sums and update SQ tags
			--AS : AS tag for genome assembly identifier
			--UR : UR tag for @SQ tag (if different from --fasta)
			--SP : SP tag for @SQ tag
			--checkSQ : check the consistency of SQ tags (SN and LN) with existing header lines. Must be used with --fasta option
	</pre>		</pre>

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	=== Example Output ===		=== Example Output ===
	<pre>		<pre>
	~~Arguments~~ in ~~effect:~~		polishBAM (options) --in=<inBamFile> --out=<outBamFile>
	~~Input file : testFiles/testSam.sam~~
	~~Output file : results/trimSam.sam~~
	~~#TrimBases : 2~~

	~~Number of records read~~ = 10
	~~Number of records written~~ = 10
	</pre>		</pre>

Mktrost: Created page with '== Trim BAM == The `trimBam` program is released as part of the StatGen Library & Tools download. `trimBam` trims the end of reads in a SAM/BAM file, chang…'

2010-10-29T18:42:12Z

Created page with '== Trim BAM == The <code>trimBam</code> program is released as part of the StatGen Library & Tools download. <code>trimBam</code> trims the end of reads in a SAM/BAM file, chang…'

New page

== Trim BAM ==
The <code>trimBam</code> program is released as part of the StatGen Library & Tools download.

<code>trimBam</code> trims the end of reads in a SAM/BAM file, changing read ends to ‘N’ and quality to ‘!’.

=== Parameters ===
<pre>
Required Parameters:
inFile : the SAM/BAM file to be read
outFile : the SAM/BAM file to be written
num-bases-to-trim-on-each-side : the number of bases/qualities to trim from each side
</pre>

=== Usage ===
trimBam [inFile] [outFile] [num-bases-to-trim-on-each-side]

=== Return Value ===
Returns the SamStatus for the reads/writes. 0 on success.

=== Example Output ===
<pre>
Arguments in effect:
Input file : testFiles/testSam.sam
Output file : results/trimSam.sam
#TrimBases : 2

Number of records read = 10
Number of records written = 10
</pre>

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