Difference between revisions of "BamUtil: trimBam"
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Returns the SamStatus for the reads/writes. 0 on success. | 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: | ||
| + | <pre> | ||
| + | ./bin trimBam testFiles/testSam.sam results/trimSam.sam 2 | ||
| + | </pre> | ||
| + | Example Output: | ||
<pre> | <pre> | ||
Arguments in effect: | Arguments in effect: | ||
| Line 43: | Line 48: | ||
</pre> | </pre> | ||
| − | + | ==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: | ||
| + | <pre> | ||
| + | ./bin trimBam testFiles/testSam.sam results/trimSam.sam -L 1 -R 2 | ||
| + | </pre> | ||
| + | Example Output: | ||
<pre> | <pre> | ||
Arguments in effect: | Arguments in effect: | ||
| Line 58: | Line 68: | ||
| − | + | ==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: | ||
| + | <pre> | ||
| + | ./bin trimBam testFiles/testSam.sam results/trimSam.sam -L 1 -R 2 --reverse | ||
| + | </pre> | ||
| + | Example Output: | ||
<pre> | <pre> | ||
Arguments in effect: | Arguments in effect: | ||
Revision as of 16:01, 14 November 2012
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 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 (or --left/--right) 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.
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 forward & reverse the same
Example Input, trimming 1 base from the left and 2 bases from the right:
./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 : 1 #Bases to trim from the right of reverse strands : 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 --reverse
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
