BamUtil: clipOverlap

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)
Clip occurs after the read ends	Entire read is soft clipped, 0-based position is left as the original (not modified)
Clip occurs before the read starts	Nothing is clipped. The read is not changed.

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), preceding insertions remain.	Entire read is soft clipped, 0-based position is left as the original (not modified)
Clip occurs before the read starts	Entire read is soft clipped, 0-based position is left as the original (not modified)
Clip occurs after the read ends	Nothing is clipped. The read is not changed.

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.