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BamUtil: trimBam (view source)

Revision as of 11:42, 3 April 2012

5 bytes removed ,  11:42, 3 April 2012
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== Trim BAM ==
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= Overview of the <code>trimBam</code> function of <code>bamUtil</code> =
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The <code>trimBam</code> program is released as part of the StatGen Library & Tools download.
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The <code>trimBam</code> option on the [[bamUtil]] executable trims the end of reads in a SAM/BAM file, changing read ends to ‘N’ and quality to ‘!’.
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<code>trimBam</code> trims the end of reads in a SAM/BAM file, changing read ends to ‘N’ and quality to ‘!’.
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= Usage =
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./bam trimBam [inFile] [outFile] [num-bases-to-trim-on-each-side]
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=== Parameters ===
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= Parameters =
 
<pre>
 
<pre>
 
     Required Parameters:
 
     Required Parameters:
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         num-bases-to-trim-on-each-side : the number of bases/qualities to trim from each side
 
         num-bases-to-trim-on-each-side : the number of bases/qualities to trim from each side
 
</pre>
 
</pre>
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=== Usage ===
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trimBam [inFile] [outFile] [num-bases-to-trim-on-each-side]
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=== Return Value ===
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= Return Value =
 
Returns the SamStatus for the reads/writes.  0 on success.
 
Returns the SamStatus for the reads/writes.  0 on success.
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=== Example Output ===
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= Example Output =
 
<pre>
 
<pre>
 
Arguments in effect:  
 
Arguments in effect:  
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</pre>
 
</pre>
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[[Category:BamUtil|trimBam]]
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[[Category:BAM Software]]
 
[[Category:Software]]
 
[[Category:Software]]
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[[Category:StatGen Download]]
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[[Category:BAM Software]]
 
Retrieved from "http://genome.sph.umich.edu/wiki/Special:MobileDiff/4753"

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