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]

Version 1.0.6 and later:

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 reverse strands are reversed and then the left & right are trimmed.

This means that --left actually trims from the right of the read in the SAM/BAM for reverse reads.

Optionally --ignoreStrand/-i can be specified to ignore the strand information and treat forward/reverse the same.

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 (or --left/--right) can be specified to indicate the number of bases to trim from the left/right (left/right are reversed for reverse strands)
    Optional Parameters:
        --ignoreStrand : ignore strand information - do not reverse left/right for reverse reads

Return Value

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

Examples

Trim the same number of bases from each side

Example Input, trimming 2 bases:

./bin trimBam testFiles/testSam.sam results/trimSam.sam 2

Example Output:

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

Trim different bases from each side, but treat reverse strands the opposite

Example Input, trimming 1 base from the left and 2 bases from the right for forward strands and do the opposite for reverse strands:

./bin trimBam testFiles/testSam.sam results/trimSam.sam -L 1 -R 2

Example Output:

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

Trim different bases from each side, but treat forward & reverse the same

Example Input, trimming 1 base from the left and 2 bases from the right ignoring strand information:

./bin trimBam testFiles/testSam.sam results/trimSam.sam -L 1 -R 2 --ignoreStrand

Example Output:

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