BamUtil: trimBam
From Genome Analysis Wiki
Trim BAM
The trimBam program is released as part of the StatGen Library & Tools download.
trimBam trims the end of reads in a SAM/BAM file, changing read ends to ‘N’ and quality to ‘!’.
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
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
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
