BamUtil: clipOverlap
Overview of the clipOverlap
function of bamUtil
The clipOverlap
option on the bamUtil executable clips overlapping read pairs.
RESTRICTIONS
This tool assumes the file is sorted by ReadName.
Rules for Clipping
Clipping from the front
The first operation after the softclip will be a Match/Mismatch, meaning that any trailing pads, deletions, insertions, or skips will also be soft clipped.
Clip Location | How it is handled |
---|---|
If the clip position falls in a skip/deletion | Removes the entire skip/deletion |
If the position immediately after the clip is a skip/deletion | Also removes the skip/deletion |
If the position immediately after the clip is an Insert | Softclips the insert |
If the position immediately after the clip is a Pad | Removes the pad |
Last match/mismatch position of the read (the entire read is clipped) | Entire read is soft clipped, 0-based position changed left as the original (not modified) |
Clipping from the back
Clip Location | How it is handled |
---|
Usage
Parameters
Required Parameters: --in : the SAM/BAM file to be read --out : the SAM/BAM file to be written Optional Parameters: --noeof : do not expect an EOF block on a bam file. --params : print the parameter settings
Input File (--in
)
Use --in
followed by your file name to specify the SAM/BAM input file.
The program automatically determines if your input file is SAM/BAM/uncompressed BAM without any input other than a filename from the user, unless your input file is stdin.
A -
is used to indicate to read from stdin and the extension is used to determine the file type (no extension indicates SAM).
SAM/BAM/Uncompressed BAM from file | --in yourFileName
|
SAM from stdin | --in - |
BAM from stdin | --in -.bam |
Uncompressed BAM from stdin | --in -.ubam |
Note: Uncompressed BAM is compressed using compression level-0 (so it is not an entirely uncompressed file). This matches the samtools
implementation so pipes between our tools and samtools
are supported.
Output File (--out
)
Use --out
followed by your file name to specify the SAM/BAM output file.
The file extension is used to determine whether to write SAM/BAM/uncompressed BAM. A -
is used to indicate stdout and the extension for file type (no extension is SAM).
SAM to file | --out yourFileName.sam
|
BAM to file | --out yourFileName.bam
|
Uncompressed BAM to file | --out yourFileName.ubam
|
SAM to stdout | --out -
|
BAM to stdout | --out -.bam
|
Uncompressed BAM to stdout | --out -.ubam
|
Note: Uncompressed BAM is compressed using compression level-0 (so it is not an entirely uncompressed file). This matches the samtools
implementation so pipes between our tools and samtools
are supported.
Return Value
Returns the SamStatus for the reads/writes.