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BamUtil (view source)

Revision as of 17:14, 11 September 2021

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= bam Executable =
+
[[Category:bamUtil]]
−
When the pipeline is compiled, the SAM/BAM executable, "bam" is generated in the pipeline/bam/ directory.
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[[Category:C++]]
 +
[[Category:Software]]
   −
The software reads the beginning of an input file to determine if it is SAM/BAM.  To determine the format (SAM/BAM) of the output file, the software checks the output file's extension.  If the extension is ".bam" it writes a BAM file, otherwise it writes a SAM file.
+
= bamUtil Overview =
 +
 
 +
bamUtil is a repository that contains several programs that perform operations on SAM/BAM files.  All of these programs are built into a single executable, <code>bam</code>.
   −
The bam executable has the following functions.
  −
* [[C++ Executable: bam#Read and Validate a SAM/BAM file|Read and Validate a SAM/BAM file]]
  −
* [[C++ Executable: bam#Read a SAM/BAM file and write as a SAM/BAM file|Read a SAM/BAM file and write as a SAM/BAM file]]
  −
* [[C++ Executable: bam#Dump a BAM index file|Dump a BAM index file into an easy to read text version]]
  −
* [[C++ Executable: bam#Read & Write indexed BAM file|Read an indexed BAM file reference by reference id -1 to 22 and write it out as a SAM/BAM file]]
     −
This executable is built using the [[C++ Library: bam|bam library]].
+
== Getting Help ==
    +
If you have any questions please use the [https://github.com/statgen/bamUtil bamUtil GitHub page] to raise and issue.
   −
== Read and Validate a SAM/BAM file ==
+
See [[BamUtil: FAQ]] to see if your question has already been answered.
   −
The <code>validate</code> option on the bam executable validates a SAM/BAM file. 
+
== Where to Find It ==
 +
{{ToolGitRepo|repoName=bamUtil}}
   −
The validation checks that the file is sorted as specified in the user options.  Default is unsorted, in which case, no order validation is done.
+
== Releases ==
   −
SAM fields are validated against: [[SAM Validation Criteria]]
+
If you prefer to run the last official release rather than the latest development version, you can download that here.
   −
'''NOTE: Currently only minimal validation is currently done.'''
+
There are two versions of the release, one that include libStatGen and one that does not.  If you already have libStatGen installed and want to use your own copy, use the version that does not include libStatGen.
   −
=== Parameters ===
+
=== Full Release (includes libStatGen) ===
−
<pre>
  −
    Required Parameters:
  −
--in : the SAM/BAM file to be validated
  −
    Optional Parameters:
  −
--noeof            : do not expect an EOF block on a bam file.
  −
--so_flag          : validate the file is sorted based on the header's @HD SO flag.
  −
--so_coord          : validate the file is sorted based on the coordinate.
  −
--so_query          : validate the file is sorted based on the query name.
  −
--quitAfterErrorNum : Number of records with errors/invalids to allow before quiting.
  −
                      -1 (default) indicates to not quit until the entire file is validated.
  −
                      0 indicates not to read/validate anything.
  −
--maxReportedErrors : Maximum number of errors to print (defaults to 100)
  −
</pre>
     −
=== Usage ===
+
To install an official release, unpack the downloaded file (tar xvf), cd into the bamUtil_x.x.x directory and type make all.
   −
./bam validate --in <inputFile> [--noeof] [--so_flag|--so_coord|--so_query] [--quitAfterErrorNum <numErrors>] [--maxReportedErrors <numReportedErrors>]
+
For version 1.0.14 and later, please download libStatGen and bamUtil separately:
      −
=== Return Value ===
+
'''Version 1.0.14 - Released 7/8/2015'''
−
*     0: all records are successfully read, are valid, and are properly sorted.
+
*[[LibStatGen Download#Official Releases|libStatGen version 1.0.14]]
−
* non-0: at least one record was not successfully read, not valid, or not properly sorted.
+
*[[#Release of just BamUtil (does not include libStatGen)|bamUtil version 1.0.14]]
      −
=== Example Output ===
+
'''Older Releases'''
−
<pre>
+
* [[Media:BamUtilLibStatGen.1.0.13.tgz|BamUtilLibStatGen.1.0.13.tgz‎]] - Released 2/20/2015
−
The following parameters are in effect:
+
** Contains: [[LibStatGen Download#Official Releases|libStatGen version 1.0.13]] - see link for version updates
 +
** Contains: [[#Release of just BamUtil (does not include libStatGen)|bamUtil version 1.0.13]] - see link for version updates
   −
Input Parameters
  −
--in [t.sam], --noeof, --quitAfterErrorNum [-1], --maxReportedErrors [100]
  −
  SortOrder : --so_flag, --so_coord, --so_query
     −
Record 1
+
* [[Media:BamUtilLibStatGen.1.0.12.tar.gz|BamUtilLibStatGen.1.0.12.tgz‎]] - Released 5/14/2014
−
FAIL_PARSE: Too few columns in the Record
+
** Contains: [[LibStatGen Download#Official Releases|libStatGen version 1.0.12]] - see link for version updates
 +
** Contains: [[#Release of just BamUtil (does not include libStatGen)|bamUtil version 1.0.12]] - see link for version updates
 +
** Adds regions to [[BamUtil: mergeBam|mergeBam]]
 +
** Accept ',' delimiters for the tags string input in [[BamUtil: squeeze|squeeze]], [[BamUtil: revert|revert]], & [[BamUtil: diff|diff]]
   −
Record 2
+
*[[Media:BamUtilLibStatGen.1.0.11.tar.gz|BamUtilLibStatGen.1.0.11.tar.gz‎]] - Released 2/28/2014
−
FAIL_PARSE: Too few columns in the Record
+
** Contains: [[LibStatGen Download#Official Releases|libStatGen version 1.0.11]] - see link for version updates
 +
** Contains: [[#Release of just BamUtil (does not include libStatGen)|bamUtil version 1.0.11]] - see link for version updates
 +
** Now properly supports 'B' & 'f' tags
 +
** Cleanup - compile issues
    +
*[[Media:BamUtilLibStatGen.1.0.10.tar.gz|BamUtilLibStatGen.1.0.10.tar.gz‎]] - Released 1/2/2014
 +
** Contains: [[LibStatGen Download#Official Releases|libStatGen version 1.0.10]] - see link for version updates
 +
** Contains: [[#Release of just BamUtil (does not include libStatGen)|bamUtil version 1.0.10]] - see link for version updates
 +
** Adds PhoneHome/Version checking.
   −
Number of records read = 2
+
*[[Media:BamUtilLibStatGen.1.0.9.tgz|BamUtilLibStatGen.1.0.9.tgz‎]] - Released 7/7/2013
−
Number of valid records = 0
+
** Contains: [[LibStatGen Download#Official Releases|libStatGen version 1.0.9]]
−
Returning: 5 (FAIL_PARSE)
+
** Contains: [[#Release of just BamUtil (does not include libStatGen)|bamUtil version 1.0.9]]
−
</pre>
+
** Update to [[BamUtil: mergeBam|mergeBam]]
 +
*** Update to ignore PG lines with duplicate IDs
 +
*** Update to accept merges of matching RG lines
 +
*** Update to log to stderr if no log/out file is specified
 +
* There is no version 1.0.8.  It was skipped to stay in line with libStatGen versions (libStatGen 1.0.8 added vcf support)
 +
*[[Media:BamUtilLibStatGen.1.0.7.tgz|BamUtilLibStatGen.1.0.7.tgz‎]] - Released 1/29/2013
 +
** Contains: [[LibStatGen Download#Official Releases|libStatGen version 1.0.7]]
 +
** Contains: [[#Release of just BamUtil (does not include libStatGen)|bamUtil version 1.0.7]]
 +
** Update to fix some compile issues on ubuntu 12.10
 +
** Update use of SamRecord::getStringTag to expect the return of a const string pointer due to libStatGen v1.0.7 updates
 +
** Update SamReferenceInfo usage due to libStatGen v1.0.7 updates
 +
** Update to [[BamUtil: diff|diff]]
 +
***  Fix DIFF to test and properly handle running out of available records.  Previously no message was printed when this happened and there was a bug for which file it freed
 +
** Update to [[BamUtil: clipOverlap|clipOverlap]]
 +
*** Update to facilitate adding other overlap handling functions
 +
** Update to [[BamUtil: mergeBam|mergeBam]] (formerly RGMergeBam)
 +
*** Rename RGMergeBam to MergeBam
 +
*** Update to handle files that already have an RG
    +
*[[Media:BamUtilLibStatGen.1.0.6.tgz|BamUtilLibStatGen.1.0.6.tgz‎]] - Released 11/14/2012
 +
** Contains: [[LibStatGen Download#Official Releases|libStatGen version 1.0.6]]
 +
** Contains: [[#Release of just BamUtil (does not include libStatGen)|bamUtil version 1.0.6]]
 +
** Update to [[BamUtil: trimBam|trimBam]]
 +
*** Update to allow trimming a different number of bases from each end of the read
 +
*[[Media:BamUtilLibStatGen.1.0.5.tgz|BamUtilLibStatGen.1.0.5.tgz‎]] - Released 10/24/2012
 +
** Contains: [[LibStatGen Download#Official Releases|libStatGen version 1.0.5]]
 +
** Contains: [[#Release of just BamUtil (does not include libStatGen)|bamUtil version 1.0.5]]
 +
** Updates to: [[BamUtil: dedup|dedup]], [[BamUtil: polishBam|polishBam]], [[BamUtil: recab|recab]]
 +
** Update to add compile option to compile without C++0x/C++11
 +
** See [[#Release of just BamUtil (does not include libStatGen)|below]] for additional details on updates
 +
*BamUtilLibStatGen.1.0.4.tgz‎ - Released skipped
 +
*[[Media:BamUtilLibStatGen.1.0.3.tgz|BamUtilLibStatGen.1.0.3.tgz‎]] - Released 09/19/2012
 +
** Contains: [[LibStatGen Download#Official Releases|libStatGen version 1.0.3]]
 +
** Contains: [[#Release of just BamUtil (does not include libStatGen)|bamUtil version 1.0.3]]
 +
** Adds: [[BamUtil: dedup|dedup]] [[BamUtil: recab|recab]]
 +
*[[Media:BamUtilLibStatGen.1.0.2.tgz|BamUtilLibStatGen.1.0.2.tgz‎]] - Released 05/16/2012
 +
** Contains: [[LibStatGen Download#Official Releases|libStatGen version 1.0.2]]
 +
** Adds: [[BamUtil: bam2FastQ|bam2FastQ]]
 +
*[[Media:BamUtilLibStatGen.1.0.1.tgz|BamUtilLibStatGen.1.0.1.tgz‎]] - Released 05/04/2012
 +
** Contains: [[LibStatGen Download#Official Releases|libStatGen version 1.0.1]]
 +
** Adds: [[BamUtil: splitBam|splitBam]], [[BamUtil: clipOverlap|clipOverlap]],  [[BamUtil: trimBam|trimBam]], [[BamUtil: polishBam|polishBam]], [[BamUtil: rgMergeBam|rgMergeBam]], [[BamUtil: gapInfo|gapInfo]]
 +
** Adds additional functionality to [[BamUtil: stats|stats]]
 +
** Adds leftShifting to [[BamUtil: writeRegion|writeRegion]] and [[BamUtil: convert|convert]]
 +
** Adds more diff fields to [[BamUtil: diff|diff]]
 +
* [[Media:BamUtilLibStatGen.1.0.0.tgz|BamUtilLibStatGen.1.0.0.tgz‎]] - Released 10/10/2011
 +
**Initial release of bamUtil that includes libStatGen version 1.0.0.  It started from the tool found in the deprecated StatGen repository.
 +
**Contains: [[LibStatGen Download#Official Releases|libStatGen version 1.0.0]] [[BamUtil: validate|validate]], [[BamUtil: convert|convert]], [[BamUtil: dumpHeader|dumpHeader]], [[BamUtil: splitChromosome|splitChromosome]], [[BamUtil: writeRegion|writeRegion]], [[BamUtil: dumpRefInfo|dumpRefInfo]], [[BamUtil: dumpIndex|dumpIndex]], [[BamUtil: readIndexedBam|readIndexedBam]], [[BamUtil: filter|filter]], [[BamUtil: readReference|readReference]], [[BamUtil: revert|revert]], [[BamUtil: diff|diff]], [[BamUtil: squeeze|squeeze]], [[BamUtil: findCigars|findCigars]], [[BamUtil: stats|stats]]
   −
== Read a SAM/BAM file and write as a SAM/BAM file ==
+
=== Release of just BamUtil (does not include libStatGen) ===
−
This executable takes 2/3 arguments.  The first argument is the input file.  The second argument is the output file.  The executable converts the first file into the format of the second file.  So if you want to convert a BAM file to a SAM file, from the pipeline/bam/ directory you just call:
  −
./bam <bamFile>.bam <newSamFile>.sam
  −
Don't forget to put in the paths to the executable and your test files.
  −
The third argument, <code>NOEOF</code>, specifies that the End-Of-File Block should not be checked for when opening the file.
     −
=== Usage ===
+
To install an official release, unpack the downloaded file (tar xvf), cd into the bamUtil_x.x.x directory and type make all.
−
./bam <inputFile> <outputFile.sam/bam/ubam (ubam is uncompressed bam)> [NOEOF]
      +
'''BamUtil.1.0.14 Release Notes'''
 +
* BamUtil Version 1.0.14 - Released 7/8/2015
 +
** https://github.com/statgen/bamUtil/archive/v1.0.14.tar.gz
 +
** Requires, but does not include: [[LibStatGen Download#Official Releases|libStatGen version 1.0.14]]
 +
** Update [[BamUtil: trimBam|trimBam]]
 +
*** Add option to soft clip (-c) instead of trimming
 +
** Update [[BamUtil: clipOverlap|clipOverlap]]
 +
*** Add option to mark reads as unmapped if they are entirely clipped
 +
** Update to [[BamUtil: bam2FastQ|bam2FastQ]]
 +
*** Add option to gzip the output files
 +
*** Add option to split Read Groups into separate fastq files
 +
*** Add option to get the quality from a tag
 +
** Update [[BamUtil: recab|recab]]
 +
*** Update to ignore ref 'N' when building the recalibration table
 +
*** Add ability to bin
 +
** Add Dedup_LowMem tool
   −
=== Return Value ===
+
'''Older Releases'''
−
Returns the SamStatus for the reads/writes.
+
* BamUtil Version 1.0.13 - Released 2/20/2015
 +
** https://github.com/statgen/bamUtil/archive/v1.0.13.tar.gz
 +
** Requires, but does not include: [[LibStatGen Download#Official Releases|libStatGen version 1.0.13]]
 +
** Makefile Updates
 +
*** Improve logic to determine actual path for the library
 +
*** Update to append to USER_COMPILE_VARS even if specified on the command line
 +
** Update [[BamUtil: writeRegion|writeRegion]]
 +
*** Add option to specify readnames to keep in a file
 +
*** Fixed bug that if a read overlapped 2 BED positions, it was printed twice
 +
** Update to [[BamUtil: bam2FastQ|bam2FastQ]]
 +
*** Update to skip non-primary reads
 +
** Update to [[BamUtil: polishBam|polishBam]]
 +
*** Update to handle '\t' string inputs and to add CO option
 +
*** Fix MD5sum calculation to convert fasta to uppercase prior to calculating
    +
* [[Media:BamUtil.1.0.12.tgz|BamUtil.1.0.12.tgz‎]] - Released 5/14/2014
 +
** Requires, but does not include: [[LibStatGen Download#Official Releases|libStatGen version 1.0.12]]
 +
** Update [[BamUtil: mergeBam|mergeBam]]
 +
*** Add a regions option
 +
** Update to [[BamUtil: squeeze|squeeze]], [[BamUtil: revert|revert]], [[BamUtil: diff|diff]]
 +
*** Also accept ',' instead of just ';' as the delimiter in the input tags string.
   −
=== Example Output ===
+
* [[Media:BamUtil.1.0.11.tgz|BamUtil.1.0.11.tgz‎]] - Released 2/28/2014
−
<pre>
+
** Requires, but does not include: [[LibStatGen Download#Official Releases|libStatGen version 1.0.11]]
−
Number of records read = 10
+
*** Adds support for 'B' & 'f' tags that did not work properly before.
−
Number of records written = 10
+
** Update [[BamUtil: splitBam|splitBam]] & [[BamUtil: polishBam|polishBam]]
−
</pre>
+
*** Update to work properly if log & output file are not specified (no longer creates '.log')
 +
** Update Main dummy/example tool to indicate the correct tool
 +
** Update to [[BamUtil: bam2FastQ|bam2FastQ]], [[BamUtil: clipOverlap|clipOverlap]], [[BamUtil: filter|filter]], [[BamUtil: mergeBam|mergeBam]], [[BamUtil: splitBam|splitBam]], [[BamUtil: squeeze|squeeze]], [[BamUtil: stats|stats]]
 +
*** Cleanup usage/parameter descriptions
 +
** Update [[BamUtil: revert|revert]]
 +
*** Update compatibility with libStatGen due to 'B' & 'f' tag handling updates
 +
** Add tests for 'B' & 'f' tags
    +
* [[Media:BamUtil.1.0.10.tar.gz|BamUtil.1.0.10.tar.gz‎]] - Released 1/2/2014
 +
** Requires, but does not include: [[LibStatGen Download#Official Releases|libStatGen version 1.0.10]]
 +
** All
 +
*** Add PhoneHome/version checking
 +
*** Make sub-program names case independent
 +
*** Fix Logger.cpp compiler warning
 +
** Adds: [[BamUtil: explainFlags|explainFlags]] - describes the SAM/BAM flags based on the flag value
 +
** Update to [[BamUtil: stats|stats]]
 +
*** Fix Stats to not try to not try to process a record after it is out of the loop (it would already have been processed or is invalid)
 +
** Update to [[BamUtil: splitBam|splitBam]]
 +
*** fix description of --noeof option
 +
** Update to [[BamUtil: writeRegion|writeRegion]]
 +
*** add exclude/required flags
 +
** Update to [[BamUtil: dedup|dedup]] & [[BamUtil: recab|recab]]
 +
*** Ignore secondary reads for dedup and making the recalibration table.
 +
*** skip QC Failures
 +
*** add excludeFlags parameters
 +
** Update to [[BamUtil: clipOverlap|clipOverlap]]
 +
*** add exclude flags
 +
*** fix bug for readName sorted when a read is filtered due to flags
 +
*** add sorting validation
 +
** Update to [[BamUtil: bam2FastQ|bam2FastQ]]
 +
*** add --merge option to generate interleaved files.
 +
*** update to open the input file before opening the output files, so if there is an error, the outputs aren't opened
 +
** Update to [[BamUtil: mergeBam|mergeBam]]
 +
*** add option to ignore the RG PI field when checking headers
 +
*** add more informative header merge error messages
   −
== Dump a BAM index file ==
+
* [[Media:BamUtil.1.0.9.tgz|BamUtil.1.0.9.tgz‎]] - Released 7/7/2013
 +
** Requires, but does not include: [[LibStatGen Download#Official Releases|libStatGen version 1.0.9]] (version 1.0.7 should also work)
 +
** Update to [[BamUtil: mergeBam|mergeBam]]
 +
*** Update to ignore PG lines with duplicate IDs
 +
*** Update to accept merges of matching RG lines
 +
*** Update to log to stderr if no log/out file is specified
   −
=== Usage ===
+
*[[Media:BamUtil.1.0.7.tgz|BamUtil.1.0.7.tgz‎]] - Released 1/29/2013
−
  ./bam dump_index <bamIndexFile>
+
** Requires, but does not include: [[LibStatGen Download#Official Releases|libStatGen version 1.0.7]] or above
 +
** Update to fix some compile issues on ubuntu 12.10
 +
** Update use of SamRecord::getStringTag to expect the return of a const string pointer due to libStatGen v1.0.7 updates
 +
** Update SamReferenceInfo usage due to libStatGen v1.0.7 updates
 +
** Update to [[BamUtil: diff|diff]]
 +
***  Fix DIFF to test and properly handle running out of available records. Previously no message was printed when this happened and there was a bug for which file it freed
 +
** Update to [[BamUtil: clipOverlap|clipOverlap]]
 +
*** Update to facilitate adding other overlap handling functions
 +
** Update to [[BamUtil: mergeBam|mergeBam]] (formerly RGMergeBam)
 +
*** Rename RGMergeBam to MergeBam
 +
*** Update to handle files that already have an RG
 +
*[[Media:BamUtil.1.0.6.tgz|BamUtil.1.0.6.tgz‎]] - Released 11/14/2012
 +
** Update to [[BamUtil: trimBam|trimBam]]
 +
*** Update to allow trimming a different number of bases from each end of the read
 +
*[[Media:BamUtil.1.0.5.tgz|BamUtil.1.0.5.tgz‎]] - Released 10/24/2012
 +
** Update to [[BamUtil: dedup|dedup]]
 +
*** Update logic for which pair to keep if they have the same quality
 +
** Update to [[BamUtil: polishBam|polishBam]]
 +
*** Update to print the number of successful header additions
 +
** Update to [[BamUtil: recab|recab]]
 +
*** Update to print the number of base skipped due to the base quality
 +
** General Updates
 +
*** Update to add compile option to compile without C++0x/C++11
 +
*BamUtil.1.0.4.tgz‎ - Released skipped
 +
*[[Media:BamUtil.1.0.3.tgz|BamUtil.1.0.3.tgz‎]] - Released 09/19/2012
 +
** Adds: [[BamUtil: dedup|dedup]] [[BamUtil: recab|recab]]
 +
** General Updates
 +
*** Update Logger to write to stderr if output is stdout
 +
** Update to [[BamUtil: stats|stats]]
 +
*** Add required/exclude flags
 +
*** Exclude Clips if excluding umapped
 +
*** Add --withinRegion flag
 +
*** Update phred/qual counts to be uint64_t instead of int to avoid overflow
 +
** Update to [[BamUtil: validate|validate]]
 +
*** Detect header failures
 +
** Update to [[BamUtil: diff|diff]]
 +
*** Update to specify chromosome/pos in ZP as a string rather than int so both can be shown
 +
** Update to [[BamUtil: readReference|readReference]]
 +
*** Output error message if the reference name is not found
 +
** Update to [[BamUtil: splitChromosome|splitChromosome]]
 +
*** Update to actually split the chromosomes and not just hard coded to output chromosomes ids 0-22
 +
** Update Makefile to have cloneLib for cloning libStatGen
 +
*[[Media:BamUtil.1.0.2.tgz|BamUtil.1.0.2.tgz‎]] - Released 05/16/2012
 +
** Adds: [[BamUtil: bam2FastQ|bam2FastQ]]
 +
*[[Media:BamUtil.1.0.1.tgz|BamUtil.1.0.1.tgz‎]] - Released 05/04/2012
 +
** Adds: [[BamUtil: splitBam|splitBam]], [[BamUtil: clipOverlap|clipOverlap]],  [[BamUtil: trimBam|trimBam]], [[BamUtil: polishBam|polishBam]], [[BamUtil: rgMergeBam|rgMergeBam]], [[BamUtil: gapInfo|gapInfo]]
 +
** Adds additional functionality to [[BamUtil: stats|stats]]
 +
** Adds leftShifting to [[BamUtil: writeRegion|writeRegion]] and [[BamUtil: convert|convert]]
 +
** Adds more diff fields to [[BamUtil: diff|diff]]
 +
*[[Media:BamUtil.1.0.0.tgz|BamUtil.1.0.0.tgz‎]] - Released 10/10/2011
 +
**Initial release of just bamUtil.  It started from the tool found in the deprecated StatGen repository.
 +
**Contains: [[BamUtil: validate|validate]], [[BamUtil: convert|convert]], [[BamUtil: dumpHeader|dumpHeader]], [[BamUtil: splitChromosome|splitChromosome]], [[BamUtil: writeRegion|writeRegion]], [[BamUtil: dumpRefInfo|dumpRefInfo]], [[BamUtil: dumpIndex|dumpIndex]], [[BamUtil: readIndexedBam|readIndexedBam]], [[BamUtil: filter|filter]], [[BamUtil: readReference|readReference]], [[BamUtil: revert|revert]], [[BamUtil: diff|diff]], [[BamUtil: squeeze|squeeze]], [[BamUtil: findCigars|findCigars]], [[BamUtil: stats|stats]]
   −
=== Return Value ===
+
== Citation ==
−
* -1 if the bam index file could not be opened.
+
If you use BamUtil, please cite our publication on GotCloud which includes BamUtil:
−
* 0 if the bam index file could be opened.
+
[http://genome.cshlp.org/content/early/2015/04/14/gr.176552.114.abstract Jun, Goo, et al. "An efficient and scalable analysis framework for variant extraction and refinement from population scale DNA sequence data." Genome research (2015): gr-176552.]
      −
== Read & Write indexed BAM file ==
+
= Programs =
   −
=== Usage ===
+
The software reads the beginning of an input file to determine if it is SAM/BAM. To determine the format (SAM/BAM) of the output file, the software checks the output file's extension.  If the extension is ".bam" it writes a BAM file, otherwise it writes a SAM file.
−
./bam read_indexed_bam <inputFilename> <outputFile.sam/bam> <bamIndexFile>
     −
=== Return Value ===
+
{{BamUtilPrograms}}
−
* 0
 
Retrieved from "http://genome.sph.umich.edu/wiki/Special:MobileDiff/1353...15169"

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