BamUtil: recab - Revision history

Mktrost: /* Required Generic Parameters */

2019-04-20T03:01:33Z

Required Generic Parameters

← Older revision		Revision as of 03:01, 20 April 2019
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	== Required Generic Parameters ==		== Required Generic Parameters ==
	{{inBAMInputFile}}		{{inBAMInputFile\|noStdin=1}}
	{{outBAMOutputFile}}		{{outBAMOutputFile}}

Mktrost: /* Handling Recalibration/Implementation Notes */

2019-04-20T03:00:41Z

Handling Recalibration/Implementation Notes

← Older revision		Revision as of 03:00, 20 April 2019
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	==Handling Recalibration/Implementation Notes==		==Handling Recalibration/Implementation Notes==

	Recalibration is a 2-step process that loops through the file twice:		Recalibration is a 2-step process that loops through the file twice (stdin is not support as input):
	# Build Recalibration Table		# Build Recalibration Table
	# Apply Recalibration Table		# Apply Recalibration Table
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	NOTE: GATK ignores/skips adapters, but our logic does not.		NOTE: GATK ignores/skips adapters, but our logic does not.


	== How to use it ==		== How to use it ==

Mktrost: /* Parameters */

2016-03-06T05:10:36Z

Parameters

← Older revision		Revision as of 05:10, 6 March 2016
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	<pre>		<pre>
	Required General Parameters :		Required General Parameters :
	--in <infile> : input BAM file name		--in <infile> : input BAM file name
	--out <outfile> : output recalibration file name		--out <outfile> : output recalibration file name
	Optional General Parameters :		Optional General Parameters :
	--log <logfile> : log and summary statistics (default: [outfile].log)		--log <logfile> : log and summary statistics (default: [outfile].log)
	--verbose : Turn on verbose mode		--verbose : Turn on verbose mode
	--noeof : do not expect an EOF block on a bam file.		--noeof : do not expect an EOF block on a bam file.
	--params : print the parameter settings		--params : print the parameter settings

	Recab Specific Required Parameters		Recab Specific Required Parameters
	--refFile <reference file> : reference file name		--refFile <reference file> : reference file name
	Recab Specific Optional Parameters :		Recab Specific Optional Parameters :
	--dbsnp <known variance file> : dbsnp file of positions		--dbsnp <known variance file> : dbsnp file of positions
	--minBaseQual <minBaseQual> : minimum base quality of bases to recalibrate (default: 5)		--minBaseQual <minBaseQual> : minimum base quality of bases to recalibrate (default: 5)
	--maxBaseQual <maxBaseQual> : maximum recalibrated base quality (default: 50)		--maxBaseQual <maxBaseQual> : maximum recalibrated base quality (default: 50)
	--blended <weight> : blended model weight		qualities over this value will be set to this value.
	--fitModel : check if the logistic regression model fits the data		This setting is applied after binning (if applicable).
	overriden by fast, but automatically applied by useLogReg		--blended <weight> : blended model weight
	--fast : use a compact representation that only allows:		--fitModel : check if the logistic regression model fits the data
	* at most 256 Read Groups		overriden by fast, but automatically applied by useLogReg
	* maximum quality 63		--fast : use a compact representation that only allows:
	* at most 127 cycles		* at most 256 Read Groups
	overrides fitModel, but is overridden by useLogReg		* maximum quality 63
	uses up to about 2.25G more memory than running without --fast.		* at most 127 cycles
	--keepPrevDbsnp : do not exclude entries where the previous base is in dbsnp when		overrides fitModel, but is overridden by useLogReg
	building the recalibration table		uses up to about 2.25G more memory than running without --fast.
	By default they are excluded from the table.		--keepPrevDbsnp : do not exclude entries where the previous base is in dbsnp when
	--keepPrevNonAdjacent : do not exclude entries where the previous base is not adjacent		building the recalibration table
	(not a Cigar M/X/=) when building the recalibration table		By default they are excluded from the table.
	By default they are excluded from the table (except the first cycle).		--keepPrevNonAdjacent : do not exclude entries where the previous base is not adjacent
	--useLogReg : use logistic regression calculated quality for the new quality		(not a Cigar M/X/=) when building the recalibration table
	automatically applies fitModel and overrides fast.		By default they are excluded from the table (except the first cycle).
	--qualField <quality tag> : tag to get the starting base quality		--useLogReg : use logistic regression calculated quality for the new quality
	(default is to get it from the Quality field)		automatically applies fitModel and overrides fast.
	--storeQualTag <quality tag> : tag to store the previous quality into		--qualField <quality tag> : tag to get the starting base quality
	--buildExcludeFlags <flag> : exclude reads with any of these flags set when building the		(default is to get it from the Quality field)
	recalibration table		--storeQualTag <quality tag> : tag to store the previous quality into
	--applyExcludeFlags <flag> : do not apply the recalibration table to any reads with any of these flags set		--buildExcludeFlags <flag> : exclude reads with any of these flags set when building the
			recalibration table. Default is 0xF04
			--applyExcludeFlags <flag> : do not apply the recalibration table to any reads with any of these flags set
			Quality Binning Parameters (optional):
			Bin qualities by phred score, into the ranges specified by binQualS or binQualF (both cannot be used)
			Ranges are specified by comma separated minimum phred score for the bin, example: 1,17,20,30,40,50,70
			The first bin always starts at 0, so does not need to be specified.
			By default, the bin value is the low end of the range.
			--binQualS : Bin the Qualities as specified (phred): minQualOfBin2, minQualofBin3...
			--binQualF : Bin the Qualities based on the specified file
			--binMid : Use the mid point of the quality bin range for the quality value of the bin.
			--binHigh : Use the high end of the quality bin range for the quality value of the bin.

	</pre>		</pre>
	{{PhoneHomeParamDesc}}		{{PhoneHomeParamDesc}}

Mktrost: /* Skip Records with any of the Specified Flags (--buildExcludeFlags, --applyExcludeFlags) */

2016-03-06T05:07:51Z

Skip Records with any of the Specified Flags (--buildExcludeFlags, --applyExcludeFlags)

← Older revision		Revision as of 05:07, 6 March 2016
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	=== Skip Records with any of the Specified Flags (<code>--buildExcludeFlags</code>, <code>--applyExcludeFlags</code>) ===		=== Skip Records with any of the Specified Flags (<code>--buildExcludeFlags</code>, <code>--applyExcludeFlags</code>) ===
	Use <code>--buildExcludeFlags</code> to skip records with any of the specified flags set when building the recalibration table, default ~~0x704~~.		Use <code>--buildExcludeFlags</code> to skip records with any of the specified flags set when building the recalibration table, default 0xF04.

	By default, when building the recalibration table reads with any of the following flags set are skipped:		By default, when building the recalibration table reads with any of the following flags set are skipped:
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	* fails QC checks		* fails QC checks
	* duplicate		* duplicate
			* supplementary alignment

	Use <code>--applyExcludeFlags</code> to skip records with any of the specified flags set when applying the recalibration table. The default value is 0x000, do not skip any reads.		Use <code>--applyExcludeFlags</code> to skip records with any of the specified flags set when applying the recalibration table. The default value is 0x000, do not skip any reads.

	~~These parameters were added in version 1.0.10.~~

	= Return Value =		= Return Value =

Mktrost at 18:05, 6 January 2014

2014-01-06T18:05:26Z

← Older revision		Revision as of 18:05, 6 January 2014
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	--applyExcludeFlags <flag> : do not apply the recalibration table to any reads with any of these flags set		--applyExcludeFlags <flag> : do not apply the recalibration table to any reads with any of these flags set
	</pre>		</pre>
			{{PhoneHomeParamDesc}}

	== Required Generic Parameters ==		== Required Generic Parameters ==

Mktrost at 17:39, 6 January 2014

2014-01-06T17:39:10Z

Show changes

Mktrost: /* Fast Recalibration (--fast) */

2013-08-02T15:24:06Z

Fast Recalibration (--fast)

← Older revision		Revision as of 15:24, 2 August 2013
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	This option cannot be used in conjunction with [[#Fit Model (--fitModel)\|<code>--fitModel</code>]], or [[#Logistic Regression (--useLogReg)\|<code>--useLogReg</code>]] and overrides [[#Fit Model (--fitModel)\|<code>--fitModel</code>]], but is overridden by [[#Logistic Regression (--useLogReg)\|<code>--useLogReg</code>]].		This option cannot be used in conjunction with [[#Fit Model (--fitModel)\|<code>--fitModel</code>]], or [[#Logistic Regression (--useLogReg)\|<code>--useLogReg</code>]] and overrides [[#Fit Model (--fitModel)\|<code>--fitModel</code>]], but is overridden by [[#Logistic Regression (--useLogReg)\|<code>--useLogReg</code>]].


	~~This option cannot be used in conjunction with [[#Fast Recalibration (--fast)\|<code>--fast</code>]] and is overriden by <code>--fast</code>, but automatically applied by useLogReg~~

	== Allow Previous Base DBSNP (<code>--keepPrevDbsnp</code>) ==		== Allow Previous Base DBSNP (<code>--keepPrevDbsnp</code>) ==

Mktrost at 17:29, 21 January 2013

2013-01-21T17:29:42Z

← Older revision		Revision as of 17:29, 21 January 2013
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	The current recalibration logic was designed for recalibrating ILLUMINA data.		The current recalibration logic was designed for recalibrating ILLUMINA data.

			NOTE: GATK ignores/skips adapters, but our logic does not.

Mktrost: /* How to use it */

2012-12-03T14:45:22Z

How to use it

← Older revision		Revision as of 14:45, 3 December 2012
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	Recommended usage with Deduper:		Recommended usage with Deduper:

	/usr/cluster/bin/bam dedup --recab --in ${INPUT}.bam --out ${OUTPUT}.bam --force --refFile ${REF} --dbsnp ${DBSNP} ~~--skipFit~~ --oneChrom --storeQualTag OQ --maxBaseQual 40		/usr/cluster/bin/bam dedup --recab --in ${INPUT}.bam --out ${OUTPUT}.bam --force --refFile ${REF} --dbsnp ${DBSNP} --oneChrom --storeQualTag OQ --maxBaseQual 40


	Recommended usage without Deduper:		Recommended usage without Deduper:

	/usr/cluster/bin/bam recab --in ${INPUT}.bam --out ${OUTPUT}.bam --refFile ${REF} --dbsnp ${DBSNP} ~~--skipFit~~ --storeQualTag OQ --maxBaseQual 40		/usr/cluster/bin/bam recab --in ${INPUT}.bam --out ${OUTPUT}.bam --refFile ${REF} --dbsnp ${DBSNP} --storeQualTag OQ --maxBaseQual 40

	= Usage =		= Usage =

Mktrost: /* How to use it */

2012-09-19T23:55:03Z

How to use it

← Older revision		Revision as of 23:55, 19 September 2012
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	Recommended usage with Deduper:		Recommended usage with Deduper:

	/usr/cluster/bin/bam dedup --recab --in ${INPUT}.bam --out ${OUTPUT}.bam --force --refFile ${REF} --dbsnp ${DBSNP} --skipFit --oneChrom --storeQualTag OQ --maxBaseQual 40		/usr/cluster/bin/bam dedup --recab --in ${INPUT}.bam --out ${OUTPUT}.bam --force --refFile ${REF} --dbsnp ${DBSNP} --skipFit --oneChrom --storeQualTag OQ --maxBaseQual 40


	Recommended usage without Deduper:		Recommended usage without Deduper:

	/usr/cluster/bin/bam recab --in ${INPUT}.bam --out ${OUTPUT}.bam --refFile ${REF} --dbsnp ${DBSNP} --skipFit --storeQualTag OQ --maxBaseQual 40		/usr/cluster/bin/bam recab --in ${INPUT}.bam --out ${OUTPUT}.bam --refFile ${REF} --dbsnp ${DBSNP} --skipFit --storeQualTag OQ --maxBaseQual 40

	= Usage =		= Usage =