BamUtil: indelDiscordance - Revision history

Mktrost at 20:10, 23 February 2012

2012-02-23T20:10:02Z

@@ Line 12: / Line 12: @@
 * Only works on one chromosome at a time
 * Repeats are single-base only
 * Skips reference positions with base 'N'
@@ Line 20: / Line 22: @@
 A position is considered to have an Insertion Discordance if at least 1 read has an insertion following this position AND at least 1 read does not AND there are at least the "minimum depth" reads at this position.
-==
+== Error Rate Algorithm ==
 = Usage =

Mktrost at 15:41, 23 February 2012

2012-02-23T15:41:06Z

← Older revision		Revision as of 11:41, 23 February 2012
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	* Skips reference positions with base 'N'		* Skips reference positions with base 'N'

	=== What is a Discordance ===		== What is a Discordance ==

	A position is considered to have a Deletion Discordance if at least 1 read has a match/mismatch AND at least 1 read has a deletion AND there are at least the "minimum depth" reads at this position.		A position is considered to have a Deletion Discordance if at least 1 read has a match/mismatch AND at least 1 read has a deletion AND there are at least the "minimum depth" reads at this position.

	A position is considered to have an Insertion Discordance if at least 1 read has an insertion following this position AND at least 1 read does not AND there are at least the "minimum depth" reads at this position.		A position is considered to have an Insertion Discordance if at least 1 read has an insertion following this position AND at least 1 read does not AND there are at least the "minimum depth" reads at this position.

			==

	= Usage =		= Usage =

Mktrost at 20:08, 22 February 2012

2012-02-22T20:08:31Z

← Older revision		Revision as of 16:08, 22 February 2012
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	= Overview of the <code>indelDiscordance</code> function of <code>bamUtil</code> =		= Overview of the <code>indelDiscordance</code> function of <code>bamUtil</code> =
	The <code>indelDiscordance</code> option on the [[bamUtil]] looks at discordance at ~~sites on~~ the ~~male~~ X ~~chromosome~~.		The <code>indelDiscordance</code> option on the [[bamUtil]] looks at insertion/deletion discordance.

			By default it looks only at the non-pseudoautosomal region of the X-Chromosome.


	== ASSUMPTIONS/RESTRICTIONS ==		== ASSUMPTIONS/RESTRICTIONS ==
			* Only works on one chromosome at a time
			* Repeats are single-base only
			* Skips reference positions with base 'N'

			=== What is a Discordance ===

			A position is considered to have a Deletion Discordance if at least 1 read has a match/mismatch AND at least 1 read has a deletion AND there are at least the "minimum depth" reads at this position.

			A position is considered to have an Insertion Discordance if at least 1 read has an insertion following this position AND at least 1 read does not AND there are at least the "minimum depth" reads at this position.

	= Usage =		= Usage =

Mktrost at 16:06, 6 February 2012

2012-02-06T16:06:25Z

← Older revision		Revision as of 12:06, 6 February 2012
Line 10:		Line 10:

	= Usage =		= Usage =
	./bam indelDiscordance --in <inputFile> [--bamIndex <bamIndexFile] [--refFile <filename>] [--umRef] [--depth minDepth] [--minRepeatLen len] [--sumRepeatLen len] [--printPos] [--chrom <name>] [--start 0basedPos] [--end 0basedPos] [--noeof] [--params]		./bam indelDiscordance --in <inputFile> [--bamIndex <bamIndexFile] [--refFile <filename>] [--umRef] [--depth minDepth] [--minRepeatLen len] [--sumRepeatLen len] [--printPos] [--chrom <name>] [--start 0basedPos] [--end 0basedPos] [--noeof] [--params]

	= Parameters =		= Parameters =
Line 25:		Line 25:
	--sumRepeatLen : all repeats this length and longer will be accumulated,		--sumRepeatLen : all repeats this length and longer will be accumulated,
	DEFAULT = 5		DEFAULT = 5
			--avgDepthMult : max depth used is the average depth * this multiplier,
			DEFAULT = 3
	--printPos : print details for each position		--printPos : print details for each position
			--printCounts : print counts of occurrances of each repeat count and of discordant cigars for each repeat count
			--sample : output the specified sample name as part of the error rate/depth table
			--gender : output the specified gender as part of the error rate/depth table
	--chrom : chromosome name other than X		--chrom : chromosome name other than X
	--start : use a 0-based inclusive start position other than the default, 2699520		--start : use a 0-based inclusive start position other than the default, 2699520

Mktrost at 21:27, 31 January 2012

2012-01-31T21:27:12Z

← Older revision		Revision as of 17:27, 31 January 2012
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	--refFile : reference file for determining repeat counts		--refFile : reference file for determining repeat counts
	--umRef : use the reference at the default UofM location, /data/local/ref/karma.ref/human.g1k.v37.umfa		--umRef : use the reference at the default UofM location, /data/local/ref/karma.ref/human.g1k.v37.umfa
	--depth : min depth at which to report indel discordance, DEFAULT >= 3		--depth : min depth at which to report indel discordance, DEFAULT >= 2
	--minRepeatLen : min repeat length for printing repeat info, DEFAULT = 1		--minRepeatLen : min repeat length for printing repeat info, DEFAULT = 1
	--sumRepeatLen : all repeats this length and longer will be accumulated,		--sumRepeatLen : all repeats this length and longer will be accumulated,

Mktrost: Created page with 'clipOverlap Category:BAM Software Category:Software = Overview of the `indelDiscordance` function of `bamUtil` = The `ind…'`


2011-12-22T21:49:06Z
Created page with 'clipOverlap Category:BAM Software Category:Software  = Overview of the <code>indelDiscordance</code> function of <code>bamUtil</code> = The <code>ind…'
New page
[[Category:BamUtil|clipOverlap]]

[[Category:BAM Software]]

[[Category:Software]]



= Overview of the <code>indelDiscordance</code> function of <code>bamUtil</code> =

The <code>indelDiscordance</code> option on the [[bamUtil]] looks at discordance at sites on the male X chromosome.



== ASSUMPTIONS/RESTRICTIONS ==





= Usage =

 ./bam indelDiscordance --in <inputFile> [--bamIndex <bamIndexFile] [--refFile <filename>] [--umRef] [--depth minDepth] [--minRepeatLen len] [--sumRepeatLen len] [--printPos] [--chrom <name>] [--start 0basedPos] [--end 0basedPos] [--noeof] [--params]



= Parameters =

<pre>

	Required Parameters:

		--in : the SAM/BAM file to calculate indelDiscordance for

	Optional Parameters:

		--bamIndex     : The path/name of the bam index file

		                 (if required and not specified, uses the --in value + ".bai")

		--refFile      : reference file for determining repeat counts

		--umRef        : use the reference at the default UofM location, 		                 /data/local/ref/karma.ref/human.g1k.v37.umfa

		--depth        : min depth at which to report indel discordance, DEFAULT >= 3

		--minRepeatLen : min repeat length for printing repeat info, DEFAULT = 1

		--sumRepeatLen : all repeats this length and longer will be accumulated,

		                 DEFAULT = 5

		--printPos     : print details for each position

		--chrom        : chromosome name other than X

		--start        : use a 0-based inclusive start position other than the default, 2699520

		--end          : use a 0-based exclusive end position other than the default, 154931043

		--noeof        : Do not expect an EOF block on a bam file.

		--params       : Print the parameter settings

</pre>





{{inBAMInputFile}}

{{bamIndex}}

{{refFile}}

{{noeofBGZFParameter}}

{{paramsParameter}}





= Return Value =







= Output =



All status messages are written to stderr.







== Example Output == 

<pre>

</pre>

BamUtil: indelDiscordance - Revision history

Mktrost at 20:10, 23 February 2012

Mktrost at 15:41, 23 February 2012

Mktrost at 20:08, 22 February 2012

Mktrost at 16:06, 6 February 2012

Mktrost at 21:27, 31 January 2012

Mktrost: Created page with 'clipOverlap Category:BAM Software Category:Software = Overview of the indelDiscordance function of bamUtil = The ind…'

Mktrost: Created page with 'clipOverlap Category:BAM Software Category:Software = Overview of the `indelDiscordance` function of `bamUtil` = The `ind…'`