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)

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)

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.