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533 bytes added
, 17:42, 3 July 2012
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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] |
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| = Parameters = | | = Parameters = |
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| 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 |
| </pre> | | </pre> |
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