Difference between revisions of "BamUtil: trimBam"
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= Usage = | = Usage = | ||
./bam trimBam [inFile] [outFile] [num-bases-to-trim-on-each-side] | ./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 '!' | ||
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outFile : the SAM/BAM file to be written | 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 | 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 | ||
</pre> | </pre> | ||
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= Example Output = | = Example Output = | ||
| + | |||
| + | If the number to trim from each side is the same: | ||
| + | <pre> | ||
| + | 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 | ||
| + | </pre> | ||
| + | |||
| + | If the number to trim from each side is different (but left/right is the same for forward/reverse): | ||
<pre> | <pre> | ||
Arguments in effect: | Arguments in effect: | ||
Input file : testFiles/testSam.sam | Input file : testFiles/testSam.sam | ||
Output file : results/trimSam.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 read = 10 | ||
Number of records written = 10 | Number of records written = 10 | ||
</pre> | </pre> | ||
| + | |||
| + | |||
| + | If the number to trim from each side is different and the reverse option is used(left/right is opposite for reverse): | ||
| + | <pre> | ||
| + | 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 | ||
| + | </pre> | ||
| + | |||
[[Category:BamUtil|trimBam]] | [[Category:BamUtil|trimBam]] | ||
[[Category:BAM Software]] | [[Category:BAM Software]] | ||
[[Category:Software]] | [[Category:Software]] | ||
Revision as of 15:42, 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]
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
