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BamUtil: recab

1,246 bytes added, 01:10, 6 March 2016
Parameters
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Required General Parameters :
--in <infile> : input BAM file name --out <outfile> : output recalibration file nameOptional General Parameters : --log <logfile> : log and summary statistics (default: [outfile].log) --verbose : Turn on verbose mode --noeof : do not expect an EOF block on a bam file. --params : print the parameter settings
Recab Specific Required Parameters
--refFile <reference file> : reference file nameRecab Specific Optional Parameters : --dbsnp <known variance file> : dbsnp file of positions --minBaseQual <minBaseQual> : minimum base quality of bases to recalibrate (default: 5) --maxBaseQual <maxBaseQual> : maximum recalibrated base quality (default: 50) qualities over this value will be set to this value. This setting is applied after binning (if applicable). --blended <weight> : blended model weight --fitModel : check if the logistic regression model fits the data overriden by fast, but automatically applied by useLogReg --fast : use a compact representation that only allows: * at most 256 Read Groups * maximum quality 63 * at most 127 cycles overrides fitModel, 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 automatically applies fitModel and overrides 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 --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. 
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