BamUtil: polishBam

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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