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= Usage =
= Usage =
./bam recab --in <InputBamFile> --out <OutputFile> [--log <logFile>] [--verbose] [--noeof] [--params] --refFile <ReferenceFile> [--dbsnp <dbsnpFile>] [--blended <weight>]
./bam recab (options) --in <InputBamFile> --out <OutputFile> [--log <logFile>] [--verbose] [--noeof] [--params] --refFile <ReferenceFile> [--dbsnp <dbsnpFile>] [--minBaseQual <minBaseQual>] [--maxBaseQual <maxBaseQual>] [--blended <weight>] [--recabLogReg]
= Parameters =
= Parameters =
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)
--maxBaseQual <maxBaseQual> : maximum recalibrated base quality (default: 50)
--blended <weight> : blended model weight
--blended <weight> : blended model weight
--recabLogReg : use logistic regression for calculating the new quality
--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
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