BamUtil: trimBam: Difference between revisions
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= | = Overview of the <code>trimBam</code> function of <code>bamUtil</code> = | ||
The <code>trimBam</code> | 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 ‘!’. | ||
= Usage = | |||
./bam trimBam [inFile] [outFile] [num-bases-to-trim-on-each-side] | |||
= Parameters = | |||
<pre> | <pre> | ||
Required Parameters: | Required Parameters: | ||
| Line 12: | Line 14: | ||
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> | ||
= Return Value = | |||
Returns the SamStatus for the reads/writes. 0 on success. | Returns the SamStatus for the reads/writes. 0 on success. | ||
= Example Output = | |||
<pre> | <pre> | ||
Arguments in effect: | Arguments in effect: | ||
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</pre> | </pre> | ||
[[Category:BamUtil|trimBam]] | |||
[[Category:BAM Software]] | |||
[[Category:Software]] | [[Category:Software]] | ||
Revision as of 11:42, 3 April 2012
Overview of the trimBam function of bamUtil
The trimBam option on the bamUtil executable trims the end of reads in a SAM/BAM file, changing read ends to ‘N’ and quality to ‘!’.
Usage
./bam trimBam [inFile] [outFile] [num-bases-to-trim-on-each-side]
Parameters
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
Return Value
Returns the SamStatus for the reads/writes. 0 on success.
Example Output
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
