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Revision as of 13:42, 29 October 2010 by Mktrost (Created page with '== 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, chang…')
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 ‘!’.
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
trimBam [inFile] [outFile] [num-bases-to-trim-on-each-side]
Returns the SamStatus for the reads/writes. 0 on success.
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