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BamUtil

913 bytes added, 20:33, 17 November 2010
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[[Category:BAM Software]]
>= bam Executable =When statgen is compiled, the SAM/BAM executable, ""bam" " is generated in the statgen/src/bin/ directory.
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.
The bam executable has the following functions.
== validate ==
The <&lt;code>&gt;validate<&lt;/code> &gt; option on the bam executable reads and validates a SAM/BAM file. This option is documented at: [[BamValidator]]
== convert ==
The <&lt;code>&gt;convert<&lt;/code> &gt; option on the bam executable reads a SAM/BAM file and writes it as a SAM/BAM file.
The executable converts the input file into the format of the output file. So if you want to convert a BAM file to a SAM file, from the pipeline/bam/ directory you just call:
./bam --in <&lt;bamFile>&gt;.bam --out <&lt;newSamFile>&gt;.sam
Don't forget to put in the paths to the executable and your test files.
=== Parameters ===
<&lt;pre>&gt;
Required Parameters:
--in : the SAM/BAM file to be read
--noeof : do not expect an EOF block on a bam file.
--params : print the parameter settings
<&lt;/pre>&gt;
=== Usage ===
./bam convert --in <&lt;inputFile> &gt; --out <&lt;outputFile.sam/bam/ubam (ubam is uncompressed bam)> &gt; [--noeof] [--params]
=== Example Output ===
<&lt;pre>&gt;
Number of records read = 10
Number of records written = 10
<&lt;/pre>&gt;
== dumpHeader ==
The <&lt;code>&gt;dumpHeader<&lt;/code> &gt; option on the bam executable prints the header of the specified SAM/BAM file to cout.
=== Parameters ===
<&lt;pre>&gt;
Required Parameters:
filename : the sam/bam filename whose header should be printed.
<&lt;/pre>&gt;
=== Usage ===
./bam dumpHeader <&lt;inputFile>&gt;
=== Return Value ===
=== Example Output ===
<&lt;pre>&gt;
@SQ SN:1 LN:247249719
@SQ SN:2 LN:242951149
@SQ SN:3 LN:199501827
<&lt;/pre>&gt;
== splitChromosome ==
The <&lt;code>&gt;splitChromosome<&lt;/code> &gt; 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 ===
<&lt;pre>&gt;
Required Parameters:
--in : the BAM file to be split
--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 + "&quot;.bai"&quot;)
--bamout : write the output files in BAM format (default).
--samout : write the output files in SAM format.
--params : print the parameter settings
<&lt;/pre>&gt;
=== Usage ===
./bam splitChromosome --in <&lt;inputFilename> &gt; --out <&lt;outputFileBaseName> &gt; [--bamIndex <&lt;bamIndexFile>&gt;] [--noeof] [--bamout|--samout] [--params]
=== Example Output ===
<&lt;pre>&gt;
Reference ID -1 has 2 records
Reference ID 0 has 5 records
Number of records = 10
Returning: 0 (SUCCESS)
<&lt;/pre>&gt;
== writeRegion ==
The <&lt;code>&gt;writeRegion<&lt;/code> &gt; 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 ===
<&lt;pre>&gt;
Required Parameters:
--in : the BAM file to be read
--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 + "&quot;.bai"&quot;)
--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)
--end : exclusive 0-based end position (defaults to -1: meaning til the end of the reference)
--params : print the parameter settings
<&lt;/pre>&gt;
=== Usage ===
./bam writeRegion --in <&lt;inputFilename> &gt; --out <&lt;outputFilename> &gt; [--bamIndex <&lt;bamIndexFile>&gt;] [--noeof] [--refName <&lt;reference Name> &gt; | --refID <&lt;reference ID>&gt;] [--start <&lt;0-based start pos>&gt;] [--end <&lt;0-based end psoition>&gt;] [--params]
=== Return Value ===
=== Example Output ===
<&lt;pre>&gt;
Wrote t.sam with 2 records.
<&lt;/pre>&gt;
== dumpRefInfo ==
The <&lt;code>&gt;dumpRefInfo<&lt;/code> &gt; option on the bam executable prints the SAM/BAM file's reference information.
=== Parameters ===
<&lt;pre>&gt;
Required Parameters:
--in : the SAM/BAM file to be read
--printRecordRefs : print the reference information for the records in the file (grouped by reference).
--params : print the parameter settings
<&lt;/pre>&gt;
=== Usage ===
./bam dumpRefInfo --in <&lt;inputFilename> &gt; [--noeof] [--printRecordRefs] [--params]
=== Return Value ===
== dumpIndex ==
The <&lt;code>&gt;dumpIndex<&lt;/code> &gt; option on the bam executable prints BAM index file in an easy to read format.
=== Parameters ===
<&lt;pre>&gt;
Required Parameters:
--bamIndex : the path/name of the bam index file to display
--summary : only print a summary - 1 line per reference.
--params : print the parameter settings
<&lt;/pre>&gt;
=== Usage ===
./bam dumpIndex --bamIndex <&lt;bamIndexFile> &gt; [--refID <&lt;ref#>&gt;] [--summary] [--params]
=== Return Value ===
== readIndexedBam ==
The <&lt;code>&gt;readIndexedBam<&lt;/code> &gt; 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 ===
<&lt;pre>&gt;
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
<&lt;/pre>&gt;
=== Usage ===
./bam readIndexedBam <&lt;inputFilename> <&gt; &lt;outputFile.sam/bam> <&gt; &lt;bamIndexFile>&gt;
=== Return Value ===
== filter ==
The <&lt;code>&gt;filter<&lt;/code> &gt; option on the bam executable filters the reads in a a SAM/BAM file. This option is documented at: [[Bam Executable: Filter]]
== readReference ==
The <&lt;code>&gt;readReference<&lt;/code> &gt; option on the bam executable prints the specified region of the reference sequence in an easy to read format.
=== Parameters ===
<&lt;pre>&gt;
Required Parameters:
--refFile : the reference
--numBases : number of bases from start to display
--params : print the parameter settings
<&lt;/pre>&gt;
=== Usage ===
./bam readReference --refFile <&lt;referenceFilename> &gt; --refName <&lt;reference Name> &gt; --start <&lt;0 based start> &gt; --end <&lt;0 based end>&gt;|--numBases <&lt;number of bases> &gt; [--params]
=== Return Value ===
=== Example Output ===
<&lt;pre>&gt;
open and prefetch reference genome /home/mktrost/data/human.g1k.v37.fa: done.
GGCAAAATGTATATAATTATGGCATGAGGTATGCAACTTTAGGCAAGGAAGCAAAAGCAGAAACCATGAAA
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