BamUtil: clipOverlap: Difference between revisions
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The <code>clipOverlap</code> option on the [[bamUtil]] executable clips overlapping read pairs. | The <code>clipOverlap</code> option on the [[bamUtil]] executable clips overlapping read pairs. | ||
= RESTRICTIONS = | |||
*Assumes the file is sorted by ReadName | |||
*Assumes only 2 reads have matching ReadNames | |||
**It matches in pairs, so if there are 3, the first 2 will be matched and compared, but the 3rd won't. If there are 4, the first 2 will be matched and the last 2 will be matched and compared. | |||
*Only mapped reads will be clipped | |||
= Rules for Clipping = | = Rules for Clipping = | ||
| Line 30: | Line 32: | ||
| Removes the pad | | Removes the pad | ||
|- | |- | ||
| | | Clip occurs at the last match/mismatch position of the read (the entire read is clipped) | ||
| Entire read is soft clipped, 0-based position | | Entire read is soft clipped, 0-based position is left as the original (not modified) | ||
|} | |} | ||
| Line 39: | Line 41: | ||
! Clip Location !! How it is handled | ! Clip Location !! How it is handled | ||
|- | |- | ||
|If the clip position falls in a skip/deletion | |||
| Removes the entire skip/deletion | |||
|- | |||
|If the position immediately before the clip is a deletion/skip/pad | |||
| Remove the deletion/skip/pad | |||
|- | |||
|If the position immediately before the clip is an insertion | |||
| Leave the insertion, even if it results in a 70M3I27S | |||
|- | |||
|Clip occurs at the first position of the read (the entire read is clipped) | |||
| Entire read is soft clipped, 0-based position is left as the original (not modified) | |||
|} | |} | ||
Revision as of 16:20, 28 October 2011
Overview of the clipOverlap function of bamUtil
The clipOverlap option on the bamUtil executable clips overlapping read pairs.
RESTRICTIONS
- Assumes the file is sorted by ReadName
- Assumes only 2 reads have matching ReadNames
- It matches in pairs, so if there are 3, the first 2 will be matched and compared, but the 3rd won't. If there are 4, the first 2 will be matched and the last 2 will be matched and compared.
- Only mapped reads will be clipped
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 |
| Clip occurs at the last match/mismatch position of the read (the entire read is clipped) | Entire read is soft clipped, 0-based position is left as the original (not modified) |
Clipping from the back
| Clip Location | How it is handled |
|---|---|
| If the clip position falls in a skip/deletion | Removes the entire skip/deletion |
| If the position immediately before the clip is a deletion/skip/pad | Remove the deletion/skip/pad |
| If the position immediately before the clip is an insertion | Leave the insertion, even if it results in a 70M3I27S |
| Clip occurs at the first position of the read (the entire read is clipped) | Entire read is soft clipped, 0-based position is left as the original (not modified) |
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.
