Template:BamUtilPrograms - Revision history

Mktrost at 15:02, 9 March 2015

2015-03-09T15:02:53Z

← Older revision		Revision as of 11:02, 9 March 2015
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	* [[BamUtil: revert\|revert]] - Revert SAM/BAM replacing the specified fields with their previous values (if known) and removes specified tags		* [[BamUtil: revert\|revert]] - Revert SAM/BAM replacing the specified fields with their previous values (if known) and removes specified tags
	* [[BamUtil: squeeze\|squeeze]] - Reduce file size by dropping OQ fields, duplicates, & specified tags, using '=' when a base matches the reference, binning quality scores, and replacing readNames with unique integers		* [[BamUtil: squeeze\|squeeze]] - Reduce file size by dropping OQ fields, duplicates, & specified tags, using '=' when a base matches the reference, binning quality scores, and replacing readNames with unique integers
	* [[BamUtil: trimBam\|trimBam]] - Trim the ends of reads in a SAM/BAM file changing read ends to 'N' and quality to '!'		* [[BamUtil: trimBam\|trimBam]] - Trim the ends of reads in a SAM/BAM file changing read ends to 'N' and quality to '!' or by doing soft clips
	* [[BamUtil: mergeBam\|mergeBam]] - Merge multiple BAMs and headers appending ReadGroupIDs if necessary		* [[BamUtil: mergeBam\|mergeBam]] - Merge multiple BAMs and headers appending ReadGroupIDs if necessary
	* [[BamUtil: polishBam\|polishBam]] - Add/update header lines & add the RG tag to each record		* [[BamUtil: polishBam\|polishBam]] - Add/update header lines & add the RG tag to each record

Mktrost at 18:24, 3 January 2014

2014-01-03T18:24:02Z

← Older revision		Revision as of 14:24, 3 January 2014
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	~~The~~ [[BamUtil~~\|BamUtil program~~]] is built using [[C++ Library: libStatGen\|libStatGen]]. Running <code>bin/bam</code> with no parameters will print the usage information for the <code>bam</code> executable. Running <code>bin/bam ''subProgram''</code> will print the usage information for the BamUtil sub-program.		[[BamUtil]] is built using [[C++ Library: libStatGen\|libStatGen]]. Running <code>bin/bam</code> with no parameters will print the usage information for the <code>bam</code> executable. Running <code>bin/bam ''subProgram''</code> will print the usage information for the BamUtil sub-program.

	'''Tools to Rewrite SAM/BAM Files: '''		'''Tools to Rewrite SAM/BAM Files: '''

Mktrost at 18:21, 3 January 2014

2014-01-03T18:21:31Z

← Older revision		Revision as of 14:21, 3 January 2014
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	The ~~following tools are part of the~~ [[BamUtil\|BamUtil program]] ~~which~~ is built using [[C++ Library: libStatGen\|libStatGen]].		The [[BamUtil\|BamUtil program]] is built using [[C++ Library: libStatGen\|libStatGen]]. Running <code>bin/bam</code> with no parameters will print the usage information for the <code>bam</code> executable. Running <code>bin/bam ''subProgram''</code> will print the usage information for the BamUtil sub-program.

	Running <code>bin/bam</code> with no parameters will print the ~~Usage~~ information for the <code>bam</code> executable. Running <code>bin/bam ''subProgram''</code> will print the usage information for the BamUtil sub-program.


	'''Tools to Rewrite SAM/BAM Files: '''		'''Tools to Rewrite SAM/BAM Files: '''
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	* [[BamUtil: findCigars\|findCigars]] - Output just the reads that contain any of the specified CIGAR operations.		* [[BamUtil: findCigars\|findCigars]] - Output just the reads that contain any of the specified CIGAR operations.
	* [[BamUtil: convert#BAM File Recovery \| BAM Recovery]] - Recover corrupted BAM files		* [[BamUtil: convert#BAM File Recovery \| BAM Recovery]] - Recover corrupted BAM files


	'''Tools to Modify & write SAM/BAM Files: '''		'''Tools to Modify & write SAM/BAM Files: '''
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	* [[BamUtil: dedup\|dedup]] - Mark or remove duplicates, can also perform recalibration		* [[BamUtil: dedup\|dedup]] - Mark or remove duplicates, can also perform recalibration
	* [[BamUtil: recab\|recab]] - Recalibrate base qualities		* [[BamUtil: recab\|recab]] - Recalibrate base qualities


	'''Informational Tools:'''		'''Informational Tools:'''
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	* [[BamUtil: gapInfo\|gapInfo]] - Print information on the gap between read pairs in a SAM/BAM File.		* [[BamUtil: gapInfo\|gapInfo]] - Print information on the gap between read pairs in a SAM/BAM File.

			'''Helper Tools to Print Information In Readable Format:'''
	''Helper Tools to Print Information In Readable Format:'''
	* [[BamUtil: dumpHeader\|dumpHeader]] - Print the SAM/BAM Header to the screen		* [[BamUtil: dumpHeader\|dumpHeader]] - Print the SAM/BAM Header to the screen
	* [[BamUtil: dumpRefInfo\|dumpRefInfo]] - Print SAM/BAM Reference Name Information from the header		* [[BamUtil: dumpRefInfo\|dumpRefInfo]] - Print SAM/BAM Reference Name Information from the header
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	* [[BamUtil: readReference\|readReference]] - Print the reference string for the specified region to the screen		* [[BamUtil: readReference\|readReference]] - Print the reference string for the specified region to the screen
	* [[BamUtil: explainFlags\|explainFlags]] - Describe SAM/BAM flags		* [[BamUtil: explainFlags\|explainFlags]] - Describe SAM/BAM flags


	'''Additional Tools:'''		'''Additional Tools:'''
	* [[BamUtil: bam2FastQ\|bam2FastQ]] - Convert the specified BAM file to fastQs.		* [[BamUtil: bam2FastQ\|bam2FastQ]] - Convert the specified BAM file to fastQs.


	'''Dummy/Example Tools:'''		'''Dummy/Example Tools:'''
	* [[BamUtil: readIndexedBam\|readIndexedBam]] - Read an indexed BAM file reference by reference id -1 to the max reference id and write it out as a SAM/BAM file		* [[BamUtil: readIndexedBam\|readIndexedBam]] - Read an indexed BAM file reference by reference id -1 to the max reference id and write it out as a SAM/BAM file


	'''ASP programs: <span style="color:#D2691E">ASP is a new format that is currently in production, so this tool is not yet available for public release.</span>'''		'''ASP programs: <span style="color:#D2691E">ASP is a new format that is currently in production, so this tool is not yet available for public release.</span>'''
	* [[BamUtil: asp \| asp]] - perform an asynchronous pileup producing an ASP file.		* [[BamUtil: asp \| asp]] - perform an asynchronous pileup producing an ASP file.
	* [[BamUtil: dumpAsp\|dumpAsp]] - perform an asynchronous pileup producing an ASP file.		* [[BamUtil: dumpAsp\|dumpAsp]] - perform an asynchronous pileup producing an ASP file.

Mktrost: Created page with " The following tools are part of the BamUtil program which is built using libStatGen. Running `bin/bam` with no parameters ..."

2014-01-03T17:41:51Z

Created page with " The following tools are part of the BamUtil program which is built using libStatGen. Running <code>bin/bam</code> with no parameters ..."

New page

The following tools are part of the [[BamUtil|BamUtil program]] which is built using [[C++ Library: libStatGen|libStatGen]].

Running <code>bin/bam</code> with no parameters will print the Usage information for the <code>bam</code> executable. Running <code>bin/bam ''subProgram''</code> will print the usage information for the BamUtil sub-program.

'''Tools to Rewrite SAM/BAM Files: '''
* [[BamUtil: convert|convert]] - Convert SAM/BAM to SAM/BAM (optionally converts between '=' & bases in the sequence
* [[BamUtil: writeRegion|writeRegion]] - Write a file with reads in the specified region and/or have the specified read name
* [[BamUtil: splitChromosome|splitChromosome]] - Split BAM into 1 file per Chromosome
* [[BamUtil: splitBam|splitBam]] - Split BAM into 1 file per Read Group
* [[BamUtil: findCigars|findCigars]] - Output just the reads that contain any of the specified CIGAR operations.
* [[BamUtil: convert#BAM File Recovery | BAM Recovery]] - Recover corrupted BAM files

'''Tools to Modify & write SAM/BAM Files: '''
* [[BamUtil: clipOverlap|clipOverlap]] - Clip overlapping read pairs in a SAM/BAM File already sorted by Coordinate or ReadName so they do not overlap
* [[BamUtil: filter|filter]] - Filter reads by soft clipping ends with too high of a mismatch percentage and by marking reads unmapped if the quality of mismatches is too high
* [[BamUtil: revert|revert]] - Revert SAM/BAM replacing the specified fields with their previous values (if known) and removes specified tags
* [[BamUtil: squeeze|squeeze]] - Reduce file size by dropping OQ fields, duplicates, & specified tags, using '=' when a base matches the reference, binning quality scores, and replacing readNames with unique integers
* [[BamUtil: trimBam|trimBam]] - Trim the ends of reads in a SAM/BAM file changing read ends to 'N' and quality to '!'
* [[BamUtil: mergeBam|mergeBam]] - Merge multiple BAMs and headers appending ReadGroupIDs if necessary
* [[BamUtil: polishBam|polishBam]] - Add/update header lines & add the RG tag to each record
* [[BamUtil: dedup|dedup]] - Mark or remove duplicates, can also perform recalibration
* [[BamUtil: recab|recab]] - Recalibrate base qualities

'''Informational Tools:'''
* [[BamUtil: validate|validate]] - Validate a SAM/BAM File, checking file format & printing statistics
* [[BamUtil: diff|diff]] - Diff 2 coordinate sorted SAM/BAM files.
* [[BamUtil: stats|stats]] - Generate some basic statistics for a SAM/BAM file
* [[BamUtil: gapInfo|gapInfo]] - Print information on the gap between read pairs in a SAM/BAM File.

''Helper Tools to Print Information In Readable Format:'''
* [[BamUtil: dumpHeader|dumpHeader]] - Print the SAM/BAM Header to the screen
* [[BamUtil: dumpRefInfo|dumpRefInfo]] - Print SAM/BAM Reference Name Information from the header
* [[BamUtil: dumpIndex|dumpIndex]] - Print BAM Index File to the screen in a readable format
* [[BamUtil: readReference|readReference]] - Print the reference string for the specified region to the screen
* [[BamUtil: explainFlags|explainFlags]] - Describe SAM/BAM flags

'''Additional Tools:'''
* [[BamUtil: bam2FastQ|bam2FastQ]] - Convert the specified BAM file to fastQs.

'''Dummy/Example Tools:'''
* [[BamUtil: readIndexedBam|readIndexedBam]] - Read an indexed BAM file reference by reference id -1 to the max reference id and write it out as a SAM/BAM file

'''ASP programs: <span style="color:#D2691E">ASP is a new format that is currently in production, so this tool is not yet available for public release.</span>'''
* [[BamUtil: asp | asp]] - perform an asynchronous pileup producing an ASP file.
* [[BamUtil: dumpAsp|dumpAsp]] - perform an asynchronous pileup producing an ASP file.

Template:BamUtilPrograms - Revision history

Mktrost at 15:02, 9 March 2015

Mktrost at 18:24, 3 January 2014

Mktrost at 18:21, 3 January 2014

Mktrost: Created page with " The following tools are part of the BamUtil program which is built using libStatGen. Running bin/bam with no parameters ..."

Mktrost: Created page with " The following tools are part of the BamUtil program which is built using libStatGen. Running `bin/bam` with no parameters ..."