Changes

From Genome Analysis Wiki
Jump to: navigation, search

BamUtil

7,449 bytes removed, 17:14, 11 September 2021
no edit summary
[[Category:bamUtil]]
[[Category:C++]]
[[Category:Software]]
[[Category:StatGen Download]]
[[Category:BAM Software]]
= bamUtil Overview =
== Where to Find It Getting Help ==The bamUtil repository is available both via release downloads (coming soon) and via github.
On If you have any questions please use the [https://github, you can both browse .com/statgen/bamUtil bamUtil GitHub page] to raise and download the latest version of the repository as well as explore the history of changesissue.
You can access the latest version with or without gitSee [[BamUtil: FAQ]] to see if your question has already been answered.
=== Using github Where to Find It =={{ToolGitRepo|repoName=bamUtil}}
If you download from github or use git to keep up to date, you also need <code>libStatGen</code>. [[C++ Library: libStatGen|Get libStatGen]].== Releases ==
==== Using Git To Track If you prefer to run the Current Development Version ====last official release rather than the latest development version, you can download that here.
===== Clone (get your own copy) =====You can create 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 git clone (copy) using: git clone https://github.com/statgen/bamUtil.gitor git clone git://github.com/statgen/bamUtil, use the version that does not include libStatGen.git
Either of these commands create a directory called <code>bamUtil</code> in the current directory.=== Full Release (includes libStatGen) ===
Then just <code>To install an official release, unpack the downloaded file (tar xvf), cd bamUtil</code> into the bamUtil_x.x.x directory and [[BamUtil#Building|compile]]type make all.
===== Get the latest Updates (update your copy) =====To update your copy to the latest For version (a major advantage of using git)1.0.14 and later, please download libStatGen and bamUtil separately:# <code>cd pathToYourCopy/bamUtil</code># <code>make clean</code># <code>git pull</code># <code>make all</code>
=== Git Refresher ===
If you decide to use git, but need a refresher, see [[How To Use Git]] or [https://statgen.sph.umich.edu/wiki/How_To_Use_Git Notes on how to use git] (if you have access)
'''Version 1.0.14 - Released 7/8/2015'''
*[[LibStatGen Download#Official Releases|libStatGen version 1.0.14]]
*[[#Release of just BamUtil (does not include libStatGen)|bamUtil version 1.0.14]]
==== Downloading From GitHub Without Git ====
Periodically download the latest copy from github from the "Downloads" link on the webpage: https://github.com/statgen/bamUtil/archives/master.
The downloaded tar file is named "statgen-bamUtil-someHexNumber'''Older Releases'''* [[Media:BamUtilLibStatGen.1.0.13.tgz|BamUtilLibStatGen.1.tar0.gz"13. The directory created when it is untared shares the same base nametgz‎]] - Released 2/20/2015** Contains: [[LibStatGen Download#Official Releases|libStatGen version 1. I recommend that you do not change the name of the directory0. If you want one called bamUtil, create a 13]] - see link to this directory. The hex number in the directory name identifies the for version updates** Contains: [[#Release of the repository that you downloaded and is necessary to easily troubleshoot any issues you encounterjust BamUtil (does not include libStatGen)|bamUtil version 1. If you must rename the directory, be sure to record the hex number that was on the download 0.13]] - see link for future reference.version updates
== Building ==
After obtaining the bamUtil repository (either by download or from github), compile the code using <code>make all</code>. This creates the executable, <code>bam</code>, in the <code>bamUtil/bin/</code> directory, the debug executable in the <code>bamUtil/bin/debug/</code> directory, and the profiling executable in the <code>bamUtil/bin/profile/</code> directory.
* [[Media:BamUtilLibStatGen.1.0.12.tar.gz|BamUtilLibStatGen.1.0.12.tgz‎]] - Released 5/14/2014
** 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]]
*[[Media:BamUtilLibStatGen.1.0.11.tar.gz|BamUtilLibStatGen.1.0.11.tar.gz‎]] - Released 2/28/2014
** 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
= Programs =*[[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.
The software reads the beginning *[[Media:BamUtilLibStatGen.1.0.9.tgz|BamUtilLibStatGen.1.0.9.tgz‎]] - Released 7/7/2013** Contains: [[LibStatGen Download#Official Releases|libStatGen version 1.0.9]] ** Contains: [[#Release of just BamUtil (does not include libStatGen)|bamUtil version 1.0.9]]** Update to [[BamUtil: mergeBam|mergeBam]]*** Update to ignore PG lines with duplicate IDs*** Update to accept merges of an input file matching RG lines*** Update to log to determine stderr if it no log/out file is specified* There is SAM/BAMno version 1.0.8. To determine the format It was skipped to stay in line with libStatGen versions (SAMlibStatGen 1.0.8 added vcf support)*[[Media:BamUtilLibStatGen.1.0.7.tgz|BamUtilLibStatGen.1.0.7.tgz‎]] - Released 1/29/BAM2013** 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 output file, the software checks the output file's extensionreturn 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. If the extension is ".bam" it writes Previously no message was printed when this happened and there was a BAM bug for which file, otherwise it writes a SAM file.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
The bam executable has the following functions*[[Media:BamUtilLibStatGen.1.0.6.tgz|BamUtilLibStatGen.1.0.6.tgz‎]] - Released 11/14/2012* * Contains: [[C++ ExecutableLibStatGen Download#Official Releases|libStatGen version 1.0.6]] ** Contains: bam[[#validateRelease 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|validate BamUtilLibStatGen.1.0.5.tgz‎]] - Read and Validate a SAMReleased 10/24/BAM file2012** 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++ Executable11** 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: bam[[LibStatGen Download#convertOfficial 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|convert BamUtilLibStatGen.1.0.2.tgz‎]] - Read a SAMReleased 05/BAM file and write as a SAM16/BAM file2012** Contains: [[LibStatGen Download#Official Releases|libStatGen version 1.0.2]]* * Adds: [[C++ ExecutableBamUtil: bam2FastQ|bam2FastQ]]*[[Media: bam#dumpHeaderBamUtilLibStatGen.1.0.1.tgz|dumpHeader BamUtilLibStatGen.1.0.1.tgz‎]] - Print SAMReleased 05/BAM header04/2012** 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 [[C++ ExecutableBamUtil: bam#splitChromosomestats|splitChromosome - Split BAM by Chromosomestats]]* * Adds leftShifting to [[C++ ExecutableBamUtil: bam#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]] - Write Released 10/10/2011**Initial release of bamUtil that includes libStatGen version 1.0.0. It started from the alignments tool found in the indexed BAM file that fall into the specified regiondeprecated 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]]* , [[C++ ExecutableBamUtil: bam#dumpRefInfo|dumpRefInfo - Print SAM/BAM Reference Information]]* , [[C++ ExecutableBamUtil: bam#dumpIndex|dumpIndex - Dump a BAM index file into an easy to read text version]]* , [[C++ ExecutableBamUtil: bam#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]]* , [[C++ ExecutableBamUtil: bam#filter|filter - Filter reads by clipping ends with too high of a mismatch percentage and by marking reads unmapped if the quality of mismatches is too high]]* , [[C++ ExecutableBamUtil: bam#readReference|readReference - Print the reference string for the specified region]]* , [[BamUtil: revert|revert]], [[C++ ExecutableBamUtil: bam#diff|diff - Print the diffs between 2 bams]], [[BamUtil: squeeze|squeeze]], [[BamUtil: findCigars|findCigars]], [[BamUtil: stats|stats]]
This executable is built using [[C++ Library: === Release of just BamUtil (does not include libStatGen]].) ===
Just running ./bam will print To install an official release, unpack the Usage information for downloaded file (tar xvf), cd into the bam executablebamUtil_x.x.x directory and type make all.
'''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
== validate =='''Older Releases'''* 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
The <code>validate<* [[Media:BamUtil.1.0.12.tgz|BamUtil.1.0.12.tgz‎]] - Released 5/code> option on the bam executable reads and validates a SAM14/BAM file2014** Requires, but does not include: [[LibStatGen Download#Official Releases|libStatGen version 1. This 0.12]]** Update [[BamUtil: mergeBam|mergeBam]]*** Add a regions option is documented at** Update to [[BamUtil: squeeze|squeeze]], [[BamUtil: revert|revert]], [[BamValidatorBamUtil: diff|diff]]*** Also accept ',' instead of just ';' as the delimiter in the input tags string.
== convert ==* [[Media:BamUtil.1.0.11.tgz|BamUtil.1.0.11.tgz‎]] - Released 2/28/2014** Requires, but does not include: [[LibStatGen Download#Official Releases|libStatGen version 1.0.11]]*** Adds support for 'B' & 'f' tags that did not work properly before.** Update [[BamUtil: splitBam|splitBam]] & [[BamUtil: polishBam|polishBam]]The <code>convert<*** Update to work properly if log & output file are not specified (no longer creates '.log')** Update Main dummy/code> option on example tool to indicate the bam executable reads a SAMcorrect 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/BAM file and writes it as a SAM/BAM file.parameter descriptions** Update [[BamUtil: revert|revert]]*** Update compatibility with libStatGen due to 'B' & 'f' tag handling updates** Add tests for 'B' & 'f' tags
The executable converts * [[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 input file into SAM/BAM flags based on the format 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 output fileloop (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. So if you want *** skip QC Failures*** add excludeFlags parameters** Update to convert [[BamUtil: clipOverlap|clipOverlap]]*** add exclude flags*** fix bug for readName sorted when a BAM file read is filtered due to flags*** add sorting validation** Update to a SAM file, just call[[BamUtil:bam2FastQ|bam2FastQ]] <pathToExe>/bam *** add --in <bamFile>merge option to generate interleaved files.bam --out <newSamFile>.samDon*** update to open the input file before opening the output files, so if there is an error, the outputs aren't forget opened** Update to put in the paths [[BamUtil: mergeBam|mergeBam]]*** add option to ignore the executable and your test files.RG PI field when checking headers*** add more informative header merge error messages
=== Sequence Representation ===* [[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)The sequence parameter options specify how ** Update to represent the sequence [[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 the reference is specified (refFile option). If the reference is not specified or seqOrig is specified, no modifications are made to the sequence. If the reference and seqBases is specified, any matches between the sequence and the reference are represented in the sequence as the appropriate base. If the reference and seqEquals log/out file is specified, any matches between the sequence and the reference are represented in the sequence as '='.
==== Examples ====*[[Media:BamUtil.1.0.7.tgz|BamUtil.1.0.7.tgz‎]] - Released 1/29/2013** 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. ExtendedCigarPreviously 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: SSMMMDDMMMIMNNNMPMSSS[[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]], Sequence[[BamUtil: trimBam|trimBam]], [[BamUtil: polishBam|polishBam]], [[BamUtil: AATAA CTAGA T AGGGrgMergeBam|rgMergeBam]], [[BamUtil: gapInfo|gapInfo]]** Adds additional functionality to [[BamUtil: stats|stats]] Reference** Adds leftShifting to [[BamUtil: writeRegion|writeRegion]] and [[BamUtil: TAACCCTA ACCCT Aconvert|convert]] Sequence with Orig** Adds more diff fields to [[BamUtil: AATAACTAGATAGGGdiff|diff]] Sequence with Bases*[[Media: BamUtil.1.0.0.tgz|BamUtil.1.0.0.tgz‎]] - Released 10/10/2011**Initial release of just bamUtil. AATAACTAGATAGGGIt started from the tool found in the deprecated StatGen repository. Sequence with Equals**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: AA======G===GGGstats|stats]]
ExtendedCigar: SSMMMDDMMMIMNNNMPMSSS== Citation == SequenceIf you use BamUtil, please cite our publication on GotCloud which includes BamUtil: AATGA CTGGA T AGGG Reference[http: TAACCCTA ACCCT A Sequence with Orig: AATGACTGGATAGGG Sequence with Bases//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): AATGACTGGATAGGG Sequence with Equals: AA=G===GG===GGGgr-176552.]
ExtendedCigar: SSMMMDDMMMIMNNNMPMSSS
Sequence: AAT=A CT=GA T AGGG
Reference: TAACCCTA ACCCT A
Sequence with Orig: AAT=ACT=GATAGGG
Sequence with Bases: AATGACTGGATAGGG
Sequence with Equals: AA======G===GGG
ExtendedCigar: SSMMMDDMMMIMNNNMPMSSS Sequence: AA=Programs == ===G= = =GGG Reference: TAACCCTA ACCCT A Sequence with Orig: AA======G===GGG Sequence with Bases: AATAACTAGATAGGG Sequence with Equals: AA======G===GGG === Parameters ===<pre> Required Parameters: --in : the SAM/BAM file to be read --out : the SAM/BAM file to be written Optional Parameters: --refFile : reference file name --noeof : do not expect an EOF block on a bam file. --params : print the parameter settings Optional Sequence Parameters (only specify one): --seqOrig : Leave the sequence as is (default & used if reference is not specified). --seqBases : Convert any '=' in the sequence to the appropriate base using the reference (requires --ref). --seqEquals : Convert any bases that match the reference to '=' (requires --ref).</pre> === Usage === ./bam convert --in <inputFile> --out <outputFile.sam/bam/ubam (ubam is uncompressed bam)> [--refFile <reference filename>] [--seqBases|--seqEquals|--seqOrig] [--noeof] [--params]  === Return Value ===Returns the SamStatus for the reads/writes. === Example Output ===<pre>Number of records read = 10Number of records written = 10</pre> == dumpHeader ==The <code>dumpHeader</code> option on the bam executable prints the header of the specified SAM/BAM file to cout.  === Parameters ===<pre> Required Parameters: filename : the sam/bam filename whose header should be printed.</pre> === Usage ===  ./bam dumpHeader <inputFile> === Return Value ===* 0: the header was successfully read and printed.* non-0: the header was not successfully read or was not printed. (Returns the SamStatus.)  === Example Output ===<pre>@SQ SN:1 LN:247249719@SQ SN:2 LN:242951149@SQ SN:3 LN:199501827</pre>  == splitChromosome == The <code>splitChromosome</code> option on the bam executable splits an indexed BAM file into multiple files based on the Chromosome (Reference Name).  The files all have the same base name, but with an _# where # corresponds with the associated reference id from the BAM file. === Parameters ===<pre> Required Parameters: --in : the BAM file to be split --out : the base filename for the SAM/BAM files to write into. Does not include the extension. _N will be appended to the basename where N indicates the Chromosome. Optional Parameters: --noeof : do not expect an EOF block on a bam file. --bamIndex : the path/name of the bam index file (if not specified, uses the --in value + ".bai") --bamout : write the output files in BAM format (default). --samout : write the output files in SAM format. --params : print the parameter settings</pre> === Usage ===  ./bam splitChromosome --in <inputFilename> --out <outputFileBaseName> [--bamIndex <bamIndexFile>] [--noeof] [--bamout|--samout] [--params]  === Return Value ===* 0: all records are successfully read and written.* non-0: at least one record was not successfully read or written. === Example Output ===<pre>Reference ID -1 has 2 recordsReference ID 0 has 5 recordsReference ID 1 has 2 recordsReference ID 2 has 1 recordsReference ID 3 has 0 recordsReference ID 4 has 0 recordsReference ID 5 has 0 recordsReference ID 6 has 0 recordsReference ID 7 has 0 recordsReference ID 8 has 0 recordsReference ID 9 has 0 recordsReference ID 10 has 0 recordsReference ID 11 has 0 recordsReference ID 12 has 0 recordsReference ID 13 has 0 recordsReference ID 14 has 0 recordsReference ID 15 has 0 recordsReference ID 16 has 0 recordsReference ID 17 has 0 recordsReference ID 18 has 0 recordsReference ID 19 has 0 recordsReference ID 20 has 0 recordsReference ID 21 has 0 recordsReference ID 22 has 0 recordsNumber of records = 10Returning: 0 (SUCCESS)</pre>  == writeRegion == The <code>writeRegion</code> option on the bam executable writes the alignments in the indexed BAM file that fall into the specified region (reference id and start/end position). === Parameters ===<pre> Required Parameters: --in : the BAM file to be read --out : the SAM/BAM file to write to Optional Parameters: --noeof : do not expect an EOF block on a bam file. --bamIndex : the path/name of the bam index file (if not specified, uses the --in value + ".bai") --refName : the BAM reference Name to read (either this or refID can be specified) --refID : the BAM reference ID to read (defaults to -1: unmapped) --start : inclusive 0-based start position (defaults to -1) --end : exclusive 0-based end position (defaults to -1: meaning til the end of the reference) --params : print the parameter settings</pre> === Usage ===  ./bam writeRegion --in <inputFilename> --out <outputFilename> [--bamIndex <bamIndexFile>] [--noeof] [--refName <reference Name> | --refID <reference ID>] [--start <0-based start pos>] [--end <0-based end psoition>] [--params] === Return Value ===* 0: all records are successfully read and written.* non-0: at least one record was not successfully read or written. === Example Output ===<pre> Wrote t.sam with 2 records.</pre>  == dumpRefInfo ==The <code>dumpRefInfo</code> option on the bam executable prints the SAM/BAM file's reference information. === Parameters ===<pre> Required Parameters: --in : the SAM/BAM file to be read Optional Parameters: --noeof : do not expect an EOF block on a bam file. --printRecordRefs : print the reference information for the records in the file (grouped by reference). --params : print the parameter settings</pre> === Usage === ./bam dumpRefInfo --in <inputFilename> [--noeof] [--printRecordRefs] [--params] === Return Value ===* 0: the file was processed successfully.* non-0: the file was not processed successfully.  == dumpIndex ==The <code>dumpIndex</code> option on the bam executable prints BAM index file in an easy to read format. === Parameters ===<pre> Required Parameters: --bamIndex : the path/name of the bam index file to display Optional Parameters: --refID : the reference ID to read, defaults to print all --summary : only print a summary - 1 line per reference. --params : print the parameter settings</pre> === Usage === ./bam dumpIndex --bamIndex <bamIndexFile> [--refID <ref#>] [--summary] [--params] === Return Value ===* 0: the BAM index file was processed successfully.* non-0: the BAM index file was not processed successfully.  == readIndexedBam ==The <code>readIndexedBam</code> option on the bam executable reads an indexed BAM file reference id by reference id -1 to the max reference id and writes it out as a SAM/BAM file. === Parameters ===<pre> Required Parameters: inputFilename - path/name of the input BAM file outputFile.sam/bam - path/name of the output file bamIndexFile - path/name of the BAM index file</pre> === Usage ===./bam readIndexedBam <inputFilename> <outputFile.sam/bam> <bamIndexFile> === Return Value ===* 0 == filter == The <code>filter</code> option on the bam executable filters the reads in a a SAM/BAM file. This option is documented at: [[Bam Executable: Filter]] == diff ==<span style="color:#D2691E">'''***Coming Soon***'''</span> The <code>diff</code> option on the bam executable prints the difference between two coordinate sorted SAM/BAM files. This can be used to compare the outputs of running a SAM/BAM through different tools/versions of tools. The <code>diff</code> tool compares records that have the same Read Name and Fragment (from the flag). If a matching ReadName & Fragment is not found, the record is considered to be different. <code>diff</code> assumes the files are coordinate sorted and uses this assumption for determining how long to store a record before determining that the other file does not contain a matching ReadName/Fragment. If the files are not coordinate sorted, this logic does not work. By default, just the chromosome/position and cigar are compared for each record. Options are available to compare:* sequence* base quality* specified tags* turn off position comparison* turn off cigar comparison === Parameters ===<pre> Required Parameters: --in1 : first coordinate sorted SAM/BAM file to be diffed --in2 : second coordinate sorted SAM/BAM file to be diffed Optional Parameters: --out : output filename, use .bam extension to output in SAM/BAM format instead of diff format. In SAMBAM format there will be 3 output files: 1) the specified name with record diffs 2) specified name with _only_<in1>.sam/bam with records only in the in1 file 3) specified name with _only_<in2>.sam/bam with records only in the in2 file --seq : diff the sequence bases. --baseQual : diff the base qualities. --tags : diff the specified Tags formatted as Tag:Type;Tag:Type;Tag:Type... --noCigar : do not diff the the cigars. --noPos : do not diff the positions. --onlyDiffs : only print the fields that are different, otherwise for any diff all the fields that are compared are printed. --recPoolSize : number of records to allow to be stored at a time, default value: 1000000 --posDiff : max base pair difference between possibly matching records100000 --noeof : do not expect an EOF block on a bam file. --params : print the parameter settings</pre> === Usage === ./bam diff --in1 <inputFile> --in2 <inputFile> [--out <outputFile>] [--baseQual] [--tags <Tag:Type[;Tag:Type]*>] [--noCigar] [--noPos] [--onlyDiffs] [--recPoolSize <int>] [--posDiff <int>] [--noeof] [--params] === Return Value ===* 0: all records are successfully read and written.* non-0: an error occurred processing the parameters or reading one of the files.e === Output Format ===2 Output Formats:# Diff Format# BAM Format ==== Diff Format ====There are 2 types of differences.* ReadName/Fragment combo is in one file, but not in the other file within the window set by recPoolSize & posDiff* ReadName/Fragment combo is in both files, but at least one of the specified fields to diff is different Each difference output consists of 2 or 3 lines. If the record only appears in one of the files, the diff is 2 lines, if it appears in both files, the diff is 3 lines. The first line of the difference output is just the read name. The 2nd and 3rd line (if present) begin with either a '<' or a '>'. If the record is from the first file (--in1), it begins with a '<'. If the record is from the 2nd file (--in2), it begins with a '>'. The 2nd line is the flag followed by the diff'd fields from one of the records. The 3rd line (if a matching record was found) is the flag followed by the diff'd fields from the matching record.  The diff'd record lines are tab separated, and are in the following order if --onlyDiffs is not specified:* '<' or '>'* flag* chrom:pos (chromosome name ':' 1 based position) - if --noPos is not specified* cigar - if --noCigar is not specified* sequence - if --seq is specified* base quality - if --baseQual is specified* tag:type:value - for each tag:type specified in --tags* ...* tag:type:value If <code>onlyDiffs</code> is specified, only the fields that are specified and are different get printed in lines 2 & 3. ===== Example Output =====Command: ../bin/bam diff --in1 testFiles/testDiff1.sam --in2 testFiles/testDiff2.sam --seq --baseQual --tags "OP:i;MD:Z" --onlyDiffs --out results/diffOrderSam.log Output:<pre>18:462+29M5I3M:F:295< a1 1:78> a1 1:741> a1 1:70 3S1M1S ACGTN ;46>> OP:i:75 MD:Z:30A0C52> a1 1:72 3S1M1S ACGTN ;47>> OP:i:75 MD:Z:30A0C5ABC> cd *:0 * * *DEF> cd *:0 * * *</pre> ==== SAM/Bam Format ====use .sam/.bam extension to output in SAM/BAM format instead of diff format. In SAM/BAM format there will be 3 output files:# the specified name with record diffs# specified name with _only_<in1>.sam/bam with records only in the in1 file# specified name with _only_<in2>.sam/bam with records only in the in2 file When a record is found in both input files, but a difference is found, the record from the first file is written with additional tags to indicate the values from the second file, using the following tags:* ZF - Flag* ZP - Pos* ZC - Cigar* ZS - Sequence* ZQ - Base Quality* ZT - Tags == readReference ==The <code>readReference</code> option on the bam executable prints the specified region of the reference sequence in an easy to read format. === Parameters ===<pre> Required Parameters: --refFile : the reference --refName : the SAM/BAM reference Name to read --start : inclusive 0-based start position (defaults to -1) Required Length Parameter (one but not both needs to be specified): --end : exclusive 0-based end position (defaults to -1: meaning til the end of the reference) --numBases : number of bases from start to display --params : print the parameter settings</pre> === Usage === ./bam readReference --refFile <referenceFilename> --refName <reference Name> --start <0 based start> --end <0 based end>|--numBases <number of bases> [--params] === Return Value ===* 0: the reference file was successfully read.* non-0: the reference file was not successfully read. === Example Output ===<pre> </pre> == stats ==The <code>stats</code> option on the bam executable generates the specified statistics on a SAM/BAM file. === Parameters ===<pre> Required Parameters: --in : the SAM/BAM file to calculate stats for Types of Statistics that can be generated: --basic : Turn on basic statistic generation --qual : Generate a count for each quality (displayed as non-phred quality) --phred : Generate a count for each quality (displayed as phred quality) --baseQC : Write per base statistics to the specified file. Optional Parameters: --maxNumReads : Maximum number of reads to process Defaults to -1 to indicate all reads. --unmapped : Only process unmapped reads (requires a bamIndex file) --bamIndex : The path/name of the bam index file (if required and not specified, uses the --in value + ".bai") --regionList : File containing the region list chr<tab>start_pos<tab>end<pos>. Positions are 0 based and the end_pos is not included in the region. Uses bamIndex. --minMapQual : The minimum mapping quality for filtering reads in the baseQC stats. --noeof : Do not expect an EOF block on a bam file. --params : Print the parameter settings</pre> For all types of statistics, the bam file used is specified by <code>--in</code>. The optional parameters are also used for all types of statistics.   === Types of Statistics === ==== Basic ====Prints summary statistics for the file:*TotalReads - # of reads that are in the file*MappedReads - # of reads marked mapped in the flag*PairedReads - # of reads marked paired in the flag*ProperPair - # of reads marked paired AND proper paired in the flag*DuplicateReads - # of reads marked duplicate in the flag*QCFailureReads - # of reads marked QC failure in the flag*MappingRate(%) - # of reads marked mapped in the flag / TotalReads*PairedReads(%) - # of reads marked paired in the flag / TotalReads*ProperPair(%) - # of reads marked paired AND proper paired in the flag / TotalReads*DupRate(%) - # of reads marked duplicate in the flag / TotalReads*QCFailRate(%) - # of reads marked QC failure in the flag / TotalReads*TotalBases - # of bases in all reads*BasesInMappedReads - # of bases in reads marked mapped in the flag   ==== Qual/Phred ====Prints a count of the number of times each quality value appears in the file.*<code>phred</code> Displays Quality as phred integers [0-93]*<code>qual</code> Displays Quality as non-phred integers (phred + 33) [33-126]  ==== BaseQC ===='''This capability is coming soon, so these notes may be updated prior to it being completed...''' Do we print stats for positions where the reference base is 'N'?? (any special note for those? Qplot would not count them in the depth.) The <code>baseQC</code> option generates the following statistics: For each position, the following counts are incremented if:# a read spans the reference position (starts before or at this reference position and ends at or after this position)# regardless of duplicate/qc failure/unmapped/mapping quality# regardless of the CIGAR for this position (other than clips at the beginning/end which are not counted, but deletions and skips are counted)*TotalReads(e6) - # of reads that span this position. *DupRate(%) - # of reads marked duplicate in the flag / TotalReads*QCFailRate(%) - # of reads marked QC failure in the flag / TotalReads*PairedReads(%) - # of reads marked paired in the flag / TotalReads*ProperPaired(%) - # of reads marked paired AND proper paired in the flag / TotalReads*MappedBases(e9) - # of reads marked mapped in the flag*MappingRate(%) - # of reads marked mapped in the flag / TotalReads*ZeroMapQual(%) - # of reads marked mapped in the flag AND have a Mapping Quality of 0 / TotalReads*MapQual<10(%) - # of reads marked mapped in the flag AND have a Mapping Quality < 10 / TotalReads*MapRate_MQpass(%) - # of reads marked mapped in the flag AND have a Mapping Quality >= a minimum Mapping Quality / TotalReads
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.
For each position, the following counts are incremented if:# a read spans the reference position (starts before or at this reference position and ends at or after this position)# the read is NOT a duplicate, qc failure, unmapped, or mapped with a mapping quality less than the min# the CIGAR for this position is a M/=/X (match/mismatch)TBD - should it count if the read has a base of 'N'*Depth - # of reads. *Q20Bases(e9) - # of bases at this position with a base quality (from the read) of Q20 or higher.*Q20BasesPct(%) - Q20Bases / Depth{{BamUtilPrograms}}

Navigation menu