Difference between revisions of "BamUtil: polishBam"

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(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…')
 
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== Trim BAM ==
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== Polish BAM ==
The <code>trimBam</code> program is released as part of the StatGen Library & Tools download.
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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:
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  Required parameters:  
         inFile  : the SAM/BAM file to be read
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         -i/--in : input BAM file
         outFile : the SAM/BAM file to be written
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        -o/--out : output BAM file
         num-bases-to-trim-on-each-side : the number of bases/qualities to trim from each side
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  Optional parameters:
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        -v : turn on verbose mode
 +
        -l/--log : writes logfile. <outBamFile>.log will be used if value is unspecified
 +
         --HD : add @HD header line
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        --RG : add @RG header line
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        --PG : add @PG header line
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        -f/--fasta : fasta reference file to compute MD5sums and update SQ tags
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        --AS : AS tag for genome assembly identifier
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         --UR : UR tag for @SQ tag (if different from --fasta)
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        --SP : SP tag for @SQ tag
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        --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:
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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>
  

Revision as of 13:46, 29 October 2010

Polish BAM

The polishBam program is released as part of the StatGen Library & Tools download.

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


Parameters

   Required parameters: 
        -i/--in : input BAM file
        -o/--out : output BAM file
   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

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

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