Difference between revisions of "BamUtil: trimBam"
From Genome Analysis Wiki
Jump to navigationJump to search| Line 1: | Line 1: | ||
| − | = | + | = 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: | ||
| Line 31: | Line 30: | ||
</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
