BamUtil: clipOverlap - Revision history

Mktrost: /* ASSUMPTIONS/RESTRICTIONS */

2016-03-06T04:01:37Z

ASSUMPTIONS/RESTRICTIONS

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	*Assumes the file is sorted by Coordinate (or ReadName if using <code>--readName</code> option)		*Assumes the file is sorted by Coordinate (or ReadName if using <code>--readName</code> option)
	*Assumes only 2 reads have matching ReadNames		*Assumes only 2 reads have matching ReadNames (Supplementary and Secondary reads are ignored/skipped by default so will not cause a problem)
	**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.		**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		*Only mapped reads will be clipped

Mktrost: /* Parameters */

2016-03-06T04:00:24Z

Parameters

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	--stats : Print some statistics on the overlaps.		--stats : Print some statistics on the overlaps.
	--overlapsOnly : Only output overlapping read pairs		--overlapsOnly : Only output overlapping read pairs
	--excludeFlags : Skip records with any of the specified flags set, default ~~0x70C~~		--excludeFlags : Skip records with any of the specified flags set, default 0xF0C
	--unmapped : Mark records that would be completely clipped as unmapped		--unmapped : Mark records that would be completely clipped as unmapped
	--noeof : Do not expect an EOF block on a bam file.		--noeof : Do not expect an EOF block on a bam file.

Mktrost: /* Skip Records with any of the Specified Flags (--excludeFlags) */

2016-03-06T03:59:46Z

Skip Records with any of the Specified Flags (--excludeFlags)

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	=== Skip Records with any of the Specified Flags (<code>--excludeFlags</code>)===		=== Skip Records with any of the Specified Flags (<code>--excludeFlags</code>)===
	Skip records with any of the specified flags set, default ~~0x70C~~		Skip records with any of the specified flags set, default 0xF0C

	By default skips reads with any of the following flags set:		By default skips reads with any of the following flags set:
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	* fails QC checks		* fails QC checks
	* duplicate		* duplicate
			* supplementary
	~~This parameter was added in version 1.0.10.~~

	=== Mark entirely clipped reads as unmapped (<code>--unmapped</code>)===		=== Mark entirely clipped reads as unmapped (<code>--unmapped</code>)===

Pjvh: /* Overview of the clipOverlap function of bamUtil */ grammar/usage.

2015-10-27T22:11:57Z

Overview of the clipOverlap function of bamUtil: grammar/usage.

Pjvh: /* Overview of the clipOverlap function of bamUtil */ Fix broken link.

2015-10-27T22:08:15Z

Overview of the clipOverlap function of bamUtil: Fix broken link.

← Older revision		Revision as of 22:08, 27 October 2015
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	When two mates overlap, this tool will clip the record's whose clipped region would has the lowest average quality.		When two mates overlap, this tool will clip the record's whose clipped region would has the lowest average quality.

	It also checks strand. If a forward strand extends past the end of a reverse strand, that will be clipped. Similarly, if a reverse strand starts before the forward strand, the region prior to the forward strand will be clipped. If the reverse strand occurs entirely before the forward strand, both strands will be entirely clipped. If the [[#Mark entirely clipped reads as unmapped (~~<code>~~--unmapped~~</code>~~)\|<code>--unmapped</code>]] option is specified rather than clipping an entire read, it will be marked as unmapped.		It also checks strand. If a forward strand extends past the end of a reverse strand, that will be clipped. Similarly, if a reverse strand starts before the forward strand, the region prior to the forward strand will be clipped. If the reverse strand occurs entirely before the forward strand, both strands will be entirely clipped. If the [[#Mark entirely clipped reads as unmapped (--unmapped)\|<code>--unmapped</code>]] option is specified rather than clipping an entire read, it will be marked as unmapped.

	The qualities on the two strands remain unchanged even with clipping.		The qualities on the two strands remain unchanged even with clipping.

Mktrost: /* Overview of the clipOverlap function of bamUtil */

2015-03-12T22:11:37Z

Overview of the clipOverlap function of bamUtil

← Older revision		Revision as of 22:11, 12 March 2015
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	When two mates overlap, this tool will clip the record's whose clipped region would has the lowest average quality.		When two mates overlap, this tool will clip the record's whose clipped region would has the lowest average quality.

	It also checks strand. If a forward strand extends past the end of a reverse strand, that will be clipped. Similarly, if a reverse strand starts before the forward strand, the region prior to the forward strand will be clipped. If the reverse strand occurs entirely before the forward strand, both strands will be entirely clipped.		It also checks strand. If a forward strand extends past the end of a reverse strand, that will be clipped. Similarly, if a reverse strand starts before the forward strand, the region prior to the forward strand will be clipped. If the reverse strand occurs entirely before the forward strand, both strands will be entirely clipped. If the [[#Mark entirely clipped reads as unmapped (<code>--unmapped</code>)\|<code>--unmapped</code>]] option is specified rather than clipping an entire read, it will be marked as unmapped.

	The qualities on the two strands remain unchanged even with clipping.		The qualities on the two strands remain unchanged even with clipping.

Mktrost: /* Parameters */

2015-03-12T22:09:33Z

Parameters

← Older revision		Revision as of 22:09, 12 March 2015
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	--overlapsOnly : Only output overlapping read pairs		--overlapsOnly : Only output overlapping read pairs
	--excludeFlags : Skip records with any of the specified flags set, default 0x70C		--excludeFlags : Skip records with any of the specified flags set, default 0x70C
	--noeof : Do not expect an EOF block on a bam file.		--unmapped : Mark records that would be completely clipped as unmapped
			--noeof : Do not expect an EOF block on a bam file.
	--params : Print the parameter settings to stderr		--params : Print the parameter settings to stderr
	Clipping By Coordinate Optional Parameters:		Clipping By Coordinate Optional Parameters:

Mktrost: /* Skip Records with any of the Specified Flags (--excludeFlags) */

2015-03-12T22:09:09Z

Skip Records with any of the Specified Flags (--excludeFlags)

← Older revision		Revision as of 22:09, 12 March 2015
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	This parameter was added in version 1.0.10.		This parameter was added in version 1.0.10.

			=== Mark entirely clipped reads as unmapped (<code>--unmapped</code>)===
			Specify this option if instead of marking reads as entirely clipped, mark them as unmapped.

			When marking a read as unmapped, it will:
			* Set CIGAR to 0
			* Set MapQ to 0
			* Clear N/A flag fields:
			** Proper pair
			** Secondary Alignment
			** Supplementary Alignment
			* Update the Mate's flag to indicate:
			** Mate Unmapped
			** Not proper pair

	{{noeofBGZFParameter}}		{{noeofBGZFParameter}}

Mktrost at 18:08, 6 January 2014

2014-01-06T18:08:09Z

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	first read in a pair to free up the record.		first read in a pair to free up the record.
	</pre>		</pre>
			{{PhoneHomeParamDesc}}

	== Required Parameters==		== Required Parameters==

Mktrost at 16:28, 6 January 2014

2014-01-06T16:28:48Z

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	* fails QC checks		* fails QC checks
	* duplicate		* duplicate

			This parameter was added in version 1.0.10.

	{{noeofBGZFParameter}}		{{noeofBGZFParameter}}

← Older revision		Revision as of 22:11, 27 October 2015
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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.

	The input file and resulting output file is sorted by coordinate (or readName if specified in the options).		The input file and resulting output file are sorted by coordinate (or readName if specified in the options).

	When a read is clipped from the front:		When a read is clipped from the front:
	* the read start position is updated to reflect the clipping		* the read start position is updated to reflect the clipping.
	* the mate's mate start position is updated to reflect the record's new position.		* the mate's mate start position is updated to reflect the record's new position.
	* the record is placed in the output file in the correct location based on the updated position.		* the record is placed in the output file in the correct location based on the updated position.

	To handle coordinate sorted files, SAM/BAM records are buffered up until it is known that all following records will have a later start position. To prevent the program from running away with memory, a limit is set to the number of records that can be buffered, see [[#Set the SAM/BAMs record buffer size (--poolSize)\|<code>--poolSize</code>]] for more information.		To handle coordinate-sorted files, SAM/BAM records are buffered up until it is known that all following records will have a later start position. To prevent the program from running away with memory, a limit is set to the number of records that can be buffered, see [[#Set the SAM/BAMs record buffer size (--poolSize)\|<code>--poolSize</code>]] for more information.

	When two mates overlap, this tool will clip the record's whose clipped region would ~~has~~ the lowest average quality.		When two mates overlap, this tool will clip the record's whose clipped region would have the lowest average quality.

	It also checks strand. If a forward strand extends past the end of a reverse strand, that will be clipped. Similarly, if a reverse strand starts before the forward strand, the region prior to the forward strand will be clipped. If the reverse strand occurs entirely before the forward strand, both strands will be entirely clipped. If the [[#Mark entirely clipped reads as unmapped (--unmapped)\|<code>--unmapped</code>]] option is specified rather than clipping an entire read, it will be marked as unmapped.		It also checks strand. If a forward strand extends past the end of a reverse strand, that will be clipped. Similarly, if a reverse strand starts before the forward strand, the region prior to the forward strand will be clipped. If the reverse strand occurs entirely before the forward strand, both strands will be entirely clipped. If the [[#Mark entirely clipped reads as unmapped (--unmapped)\|<code>--unmapped</code>]] option is specified, then rather than clipping an entire read, it will be marked as unmapped.

	The qualities on the two strands remain unchanged even with clipping.		The qualities on the two strands remain unchanged even with clipping.
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	**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.		**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		*Only mapped reads will be clipped
	*~~Mate~~ information in records are accurate		*Assumes that mate information in records are accurate

	= Rules for Clipping =		= Rules for Clipping =