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== 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, changing read ends to ‘N’ and quality to ‘!’.
=== Parameters ===
<pre>
Required Parameters:
inFile : the SAM/BAM file to be read
outFile : the SAM/BAM file to be written
num-bases-to-trim-on-each-side : the number of bases/qualities to trim from each side
</pre>
=== 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 ===
<pre>
Arguments in effect:
Input file : testFiles/testSam.sam
Output file : results/trimSam.sam
#TrimBases : 2
Number of records read = 10
Number of records written = 10
</pre>
[[Category:Software]]
[[Category:StatGen Download]]
[[Category:BAM Software]]
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, changing read ends to ‘N’ and quality to ‘!’.
=== Parameters ===
<pre>
Required Parameters:
inFile : the SAM/BAM file to be read
outFile : the SAM/BAM file to be written
num-bases-to-trim-on-each-side : the number of bases/qualities to trim from each side
</pre>
=== 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 ===
<pre>
Arguments in effect:
Input file : testFiles/testSam.sam
Output file : results/trimSam.sam
#TrimBases : 2
Number of records read = 10
Number of records written = 10
</pre>
[[Category:Software]]
[[Category:StatGen Download]]
[[Category:BAM Software]]
