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Not all bases are used for building the Recalibration table. Only bases meeting the following criteria are used:
Not all bases are used for building the Recalibration table. Only bases meeting the following criteria are used:
* Base is a CIGAR Match/Mismatch
* Base is a q Match/Mismatch
* Previous base is a CIGAR Match/Mismatch or it is the first cycle
* Previous base is a CIGAR Match/Mismatch or it is the first cycle
* Base position is not a dbSNP position
* Base position is not a dbSNP position
= Usage =
= Usage =
./bam recab (options) --in <InputBamFile> --out <OutputFile> [--log <logFile>] [--verbose] [--noeof] [--params] --refFile <ReferenceFile> [--dbsnp <dbsnpFile>] [--minBaseQual <minBaseQual>] [--maxBaseQual <maxBaseQual>] [--blended <weight>] [--useLogReg]
./bam recab (options) --in <InputBamFile> --out <OutputFile> [--log <logFile>] [--verbose] [--noeof] [--params] --refFile <ReferenceFile> [--dbsnp <dbsnpFile>] [--minBaseQual <minBaseQual>] [--maxBaseQual <maxBaseQual>] [--blended <weight>] [--skipFitModel] [--fast] [--keepPrevDbsnp] [--keepPrevNonAdjacent] [--useLogReg]
= Parameters =
= Parameters =
--maxBaseQual <maxBaseQual> : maximum recalibrated base quality (default: 50)
--maxBaseQual <maxBaseQual> : maximum recalibrated base quality (default: 50)
--blended <weight> : blended model weight
--blended <weight> : blended model weight
--useLogReg : use logistic regression for calculating the new quality
--skipFitModel : do not check if the logistic regression model fits the data
--qualField <quality tag> : tag to get the starting base quality (default is to get it from the Quality field
--fast : use a compact representation that only allows:
* at most 256 Read Groups
* maximum quality 63
* at most 127 cycles
automatically enables skipFitModel, but is overridden by useLogReg
uses up to about 2.25G more memory than running without --fast.
--keepPrevDbsnp : do not exclude entries where the previous base is in dbsnp when
building the recalibration table
By default they are excluded from the table.
--keepPrevNonAdjacent : do not exclude entries where the previous base is not adjacent
(not a Cigar M/X/=) when building the recalibration table
By default they are excluded from the table (except the first cycle).
--useLogReg : use logistic regression calculated quality for the new quality
ignores setting of skipFitModel and fast.
--qualField <quality tag> : tag to get the starting base quality
(default is to get it from the Quality field)
--storeQualTag <quality tag> : tag to store the previous quality into
--storeQualTag <quality tag> : tag to store the previous quality into
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