BamUtil: trimBam - Revision history

Mktrost: /* Soft Clipping Notes (--clip/-c) */

2017-11-13T03:28:36Z

Soft Clipping Notes (--clip/-c)

← Older revision		Revision as of 03:28, 13 November 2017
Line 20:		Line 20:

	== Soft Clipping Notes (--clip/-c) ==		== Soft Clipping Notes (--clip/-c) ==
	~~(Version~~ 1.0.14 and later)		Available in version 1.0.14 and later.

	When soft clipping:		When soft clipping:
	:* if the entire read would be soft clipped, no clipping is done, and instead the read is marked as unmapped		:* if the entire read would be soft clipped, no clipping is done, and instead the read is marked as unmapped

Mktrost: /* Soft Clipping Notes (--clip/-c) */

2017-11-13T03:28:02Z

Soft Clipping Notes (--clip/-c)

← Older revision		Revision as of 03:28, 13 November 2017
Line 20:		Line 20:

	== Soft Clipping Notes (--clip/-c) ==		== Soft Clipping Notes (--clip/-c) ==
			(Version 1.0.14 and later)
	When soft clipping:		When soft clipping:
	:* if the entire read would be soft clipped, no clipping is done, and instead the read is marked as unmapped		:* if the entire read would be soft clipped, no clipping is done, and instead the read is marked as unmapped
Line 44:		Line 45:
	# Run samtools fixmate and pipe it into samtools sort by position		# Run samtools fixmate and pipe it into samtools sort by position
	#* <pre> samtools fixmate tempQuerySort.bam - \| samtools sort - finalResult</pre>		#* <pre> samtools fixmate tempQuerySort.bam - \| samtools sort - finalResult</pre>


	= Parameters =		= Parameters =

Mktrost at 19:04, 12 March 2015

2015-03-12T19:04:33Z

← Older revision		Revision as of 19:04, 12 March 2015
Line 18:		Line 18:
	trimBam will modify the sequences to 'N', and the quality string to '!' unless the optional parameter --clip/-c is specified. If --clip/-c is specified, the ends will be soft clipped instead of modified.		trimBam will modify the sequences to 'N', and the quality string to '!' unless the optional parameter --clip/-c is specified. If --clip/-c is specified, the ends will be soft clipped instead of modified.

	~~When soft clipping~~ (--clip/-c):
	* if the entire read would be soft clipped, no clipping is done, and instead the read is marked as unmapped		== Soft Clipping Notes (--clip/-c) ==
	* mate information is not updated (start positions/mapping may change after soft clipping)		When soft clipping:
	** run samtools fixmate to fix mate information (will first need to sort by read name)		:* if the entire read would be soft clipped, no clipping is done, and instead the read is marked as unmapped
	* output is not sorted (start positions/mapping may change after soft clipping)		:* mate information is not updated (start positions/mapping may change after soft clipping)
	** run samtools sort to resort by coordinate (after fixmate)		:** run samtools fixmate to fix mate information (will first need to sort by read name)
	* soft clips already in the read are maintained or added to		:* output is not sorted (start positions/mapping may change after soft clipping)
	** if 3 bases were clipped and 2 are specified to be clipped, no change is made to that end		:** run samtools sort to resort by coordinate (after fixmate)
	** if 3 bases were clipped and 5 are specified to be clipped, 2 additional bases are clipped from that end		:* soft clips already in the read are maintained or added to
			:** if 3 bases were clipped and 2 are specified to be clipped, no change is made to that end
			:** if 3 bases were clipped and 5 are specified to be clipped, 2 additional bases are clipped from that end

			=== Fixing the mate/resorting ===
			In order to update the mate, samtools fixmate must be run.

			In order to reorder the file, samtools sort must be run.

			Notes about the samtools programs:
			* samtools fixmate requires the file to be sorted by query name.
			* samtools sort cannot write to pipes.

			====Steps====
			# Run this program and pipe it into samtools sort by query name
			#* <pre>./bam trimBam <your InputFile> - [#basesToTrim] [any other options] -c \| samtools sort -n - tempQuerySort</pre>
			# Run samtools fixmate and pipe it into samtools sort by position
			#* <pre> samtools fixmate tempQuerySort.bam - \| samtools sort - finalResult</pre>


	= Parameters =		= Parameters =
Line 68:		Line 86:

	=== SoftClip the Ends (<code>--clip</code> or <code>-c</code>) ===		=== SoftClip the Ends (<code>--clip</code> or <code>-c</code>) ===
	Use <code>--clip</code> or <code>-c</code> to soft clip the ends instead of setting to N/!.		Use <code>--clip</code> or <code>-c</code> to soft clip the ends instead of setting to N/! (or set to unmapped if the entire read would be soft clipped).

	~~When clipping:~~
	* output is not sorted (~~start positions may change after soft clipping)~~
	* soft clips already in the read are maintained or ~~added~~ to
	** if 3 bases were clipped and 2 are specified to be clipped, no change is made to that end
	** if 3 bases were clipped and 5 are specified to be clipped, 2 additional bases are clipped from that end
	* if the entire read would be soft clipped~~, no clipping is done, and instead the read is marked as unmapped~~

			See [[#Soft Clipping Notes (--clip/-c)\|Soft Clipping Notes]] for more information about clipping and post processing that will need to be done.

	{{noeofBGZFParameter}}		{{noeofBGZFParameter}}

Mktrost: /* Usage */

2015-03-12T18:51:50Z

Usage

← Older revision		Revision as of 18:51, 12 March 2015
Line 19:		Line 19:

	When soft clipping (--clip/-c):		When soft clipping (--clip/-c):
	* output is not sorted (start positions may change after soft clipping)		* if the entire read would be soft clipped, no clipping is done, and instead the read is marked as unmapped
			* mate information is not updated (start positions/mapping may change after soft clipping)
			** run samtools fixmate to fix mate information (will first need to sort by read name)
			* output is not sorted (start positions/mapping may change after soft clipping)
			** run samtools sort to resort by coordinate (after fixmate)
	* soft clips already in the read are maintained or added to		* soft clips already in the read are maintained or added to
	** if 3 bases were clipped and 2 are specified to be clipped, no change is made to that end		** if 3 bases were clipped and 2 are specified to be clipped, no change is made to that end
	** if 3 bases were clipped and 5 are specified to be clipped, 2 additional bases are clipped from that end		** if 3 bases were clipped and 5 are specified to be clipped, 2 additional bases are clipped from that end
	* if the entire read would be soft clipped, no clipping is done, and instead the read is marked as unmapped

	= Parameters =		= Parameters =

Mktrost: /* Optional parameters */

2015-03-09T15:36:57Z

Optional parameters

← Older revision		Revision as of 15:36, 9 March 2015
Line 62:		Line 62:

	=== Ignore the Strand when Trimming (<code>--ignoreStrand</code> or <code>-i</code>) ===		=== Ignore the Strand when Trimming (<code>--ignoreStrand</code> or <code>-i</code>) ===
	Use <code>--ignoreStrand</code> or <code>--i</code> to ignore the strand information and treat forward/~~reverese~~ the same. When <code>--ignoreStrand</code> or <code>--i</code> is set, do not reverse reverse reads prior to trimming left/right.		Use <code>--ignoreStrand</code> or <code>-i</code> to ignore the strand information and treat forward/reverse the same. When <code>--ignoreStrand</code> or <code>-i</code> is set, do not reverse reverse reads prior to trimming left/right.

	=== SoftClip the Ends (<code>--clip</code> or <code>-c</code>) ===		=== SoftClip the Ends (<code>--clip</code> or <code>-c</code>) ===

Mktrost: /* Parameters */

2015-03-09T15:08:44Z

Parameters

← Older revision		Revision as of 15:08, 9 March 2015
Line 34:		Line 34:
	Optional Parameters:		Optional Parameters:
	--ignoreStrand : ignore strand information - do not reverse left/right for reverse reads		--ignoreStrand : ignore strand information - do not reverse left/right for reverse reads
			--clip : soft clip the ends rather than setting to N/!
	</pre>		</pre>
	{{PhoneHomeParamDesc}}		{{PhoneHomeParamDesc}}
Line 46:		Line 47:
	If the 3rd argument a number (with no flag/option), it is the number of bases to trim from each end of the reads.		If the 3rd argument a number (with no flag/option), it is the number of bases to trim from each end of the reads.

	===Trim Bases from the Left (<code>--left</code> or <code>--L</code>)===		===Trim Bases from the Left (<code>--left</code> or <code>-L</code>)===
	Use <code>--left</code> or <code>--L</code> followed by the number of bases to be trimmed from the left.		Use <code>--left</code> or <code>-L</code> followed by the number of bases to be trimmed from the left.

	By default reverse strands are reversed and then the left is trimmed, meaning that <code>--left</code> actually trims from the right of the read in the SAM/BAM for reverse reads.		By default reverse strands are reversed and then the left is trimmed, meaning that <code>--left</code> actually trims from the right of the read in the SAM/BAM for reverse reads.

	Use [[#Ignore the Strand when Trimming (--ignoreStrand or --i)\|--ignoreStrand/-i]] to ignore the strand information and treat forward/reverse the same.		Use [[#Ignore the Strand when Trimming (--ignoreStrand or -i)\|--ignoreStrand/-i]] to ignore the strand information and treat forward/reverse the same.

	===Trim Bases from the Right (<code>--right</code> or <code>--R</code>)===		===Trim Bases from the Right (<code>--right</code> or <code>-R</code>)===
	Use <code>--right</code> or <code>--R</code> followed by the number of bases to be trimmed from the right.		Use <code>--right</code> or <code>-R</code> followed by the number of bases to be trimmed from the right.

	By default reverse strands are reversed and then the right is trimmed, meaning that <code>--right</code> actually trims from the left of the read in the SAM/BAM for reverse reads.		By default reverse strands are reversed and then the right is trimmed, meaning that <code>--right</code> actually trims from the left of the read in the SAM/BAM for reverse reads.

	Use [[#Ignore the Strand when Trimming (--ignoreStrand or --i)\|--ignoreStrand/-i]] to ignore the strand information and treat forward/reverse the same.		Use [[#Ignore the Strand when Trimming (--ignoreStrand or -i)\|--ignoreStrand/-i]] to ignore the strand information and treat forward/reverse the same.

	=== Ignore the Strand when Trimming (<code>--ignoreStrand</code> or <code>--i</code>) ===		=== Ignore the Strand when Trimming (<code>--ignoreStrand</code> or <code>-i</code>) ===
	Use <code>--ignoreStrand</code> or <code>--i</code> to ignore the strand information and treat forward/reverese the same. When <code>--ignoreStrand</code> or <code>--i</code> is set, do not reverse reverse reads prior to trimming left/right.		Use <code>--ignoreStrand</code> or <code>--i</code> to ignore the strand information and treat forward/reverese the same. When <code>--ignoreStrand</code> or <code>--i</code> is set, do not reverse reverse reads prior to trimming left/right.

			=== SoftClip the Ends (<code>--clip</code> or <code>-c</code>) ===
			Use <code>--clip</code> or <code>-c</code> to soft clip the ends instead of setting to N/!.

			When clipping:
			* output is not sorted (start positions may change after soft clipping)
			* soft clips already in the read are maintained or added to
			** if 3 bases were clipped and 2 are specified to be clipped, no change is made to that end
			** if 3 bases were clipped and 5 are specified to be clipped, 2 additional bases are clipped from that end
			* if the entire read would be soft clipped, no clipping is done, and instead the read is marked as unmapped


	{{noeofBGZFParameter}}		{{noeofBGZFParameter}}

Mktrost: /* Usage */

2015-03-09T15:05:26Z

Usage

← Older revision		Revision as of 15:05, 9 March 2015
Line 16:		Line 16:
	Optionally --ignoreStrand/-i can be specified to ignore the strand information and treat forward/reverse the same.		Optionally --ignoreStrand/-i can be specified to ignore the strand information and treat forward/reverse the same.

	trimBam will modify the sequences to 'N', and the quality string to '!'		trimBam will modify the sequences to 'N', and the quality string to '!' unless the optional parameter --clip/-c is specified. If --clip/-c is specified, the ends will be soft clipped instead of modified.

			When soft clipping (--clip/-c):
			* output is not sorted (start positions may change after soft clipping)
			* soft clips already in the read are maintained or added to
			** if 3 bases were clipped and 2 are specified to be clipped, no change is made to that end
			** if 3 bases were clipped and 5 are specified to be clipped, 2 additional bases are clipped from that end
			* if the entire read would be soft clipped, no clipping is done, and instead the read is marked as unmapped

	= Parameters =		= Parameters =

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

2015-03-09T15:03:29Z

Overview of the trimBam function of bamUtil

← Older revision		Revision as of 15:03, 9 March 2015
Line 1:		Line 1:
	= Overview of the <code>trimBam</code> function of <code>bamUtil</code> =		= Overview of the <code>trimBam</code> function of <code>bamUtil</code> =
	The <code>trimBam</code> option on the [[bamUtil]] executable trims the end of reads in a SAM/BAM file, changing read ends to ‘N’ and quality to ‘!’.		The <code>trimBam</code> option on the [[bamUtil]] executable trims the end of reads in a SAM/BAM file, changing read ends to ‘N’ and quality to ‘!’, or by soft clipping (if command-line option, <code>--clip</code> is specified).


	= Usage =		= Usage =

Mktrost: /* Required Parameters */

2014-01-06T20:58:11Z

Required Parameters

@@ Line 33: / Line 33: @@
 == Required Parameters==
-The first argument is the name of the SAM/BAM input file.
+{{InBAMInputFile|noParam=1st}}
 ==Optional parameters==
 === Number of Bases to Trim from Each End (3rd argument) ===

Mktrost at 18:07, 6 January 2014

2014-01-06T18:07:09Z

← Older revision		Revision as of 18:07, 6 January 2014
Line 30:		Line 30:
	--ignoreStrand : ignore strand information - do not reverse left/right for reverse reads		--ignoreStrand : ignore strand information - do not reverse left/right for reverse reads
	</pre>		</pre>
			{{PhoneHomeParamDesc}}

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