Difference between revisions of "BamUtil: trimBam"
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Revision as of 11:54, 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
