BamUtil: trimBam

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]

Alternately, the number of bases from each side can be specified (either or both -L/-R (--left/--right) can be specified):

./bam trimBam [inFile] [outFile] -L [num-bases-to-trim-from-left] -R [num-bases-to-trim-from-right]

By default Left/Right is as the reads are in the SAM/BAM file.

Optionally --reverse/-r can be specified to reverse the left/right for reverse reads

trimBam will modify the sequences to 'N', and the quality string 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
    Instead of num-bases-to-trim-on-each-side, -L/-R can be specified to indicate the number of bases to trim from the left/right
    Optional Parameters:
        --reverse : reverse the left/right for reverse reads

Return Value

Returns the SamStatus for the reads/writes. 0 on success.

Example Output

If the number to trim from each side is the same:

Arguments in effect: 
	Input file : testFiles/testSam.sam
	Output file : results/trimSam.sam
	#Bases to trim from each side : 2

Number of records read = 10
Number of records written = 10

If the number to trim from each side is different (but left/right is the same for forward/reverse):

Arguments in effect: 
	Input file : testFiles/testSam.sam
	Output file : results/trimSam.sam
	#Bases to trim from the left of forward strands : 1
	#Bases to trim from the right of forward strands: 2
	#Bases to trim from the left of reverse strands : 1
	#Bases to trim from the right of reverse strands : 2

Number of records read = 10
Number of records written = 10

If the number to trim from each side is different and the reverse option is used(left/right is opposite for reverse):

Arguments in effect: 
	Input file : testFiles/testSam.sam
	Output file : results/trimSam.sam
	#Bases to trim from the left of forward strands : 1
	#Bases to trim from the right of forward strands: 2
	#Bases to trim from the left of reverse strands : 2
	#Bases to trim from the right of reverse strands : 1

Number of records read = 10
Number of records written = 10