Changes

= Usage =

= Usage =

  ./bam dedup --in <InputBamFile> --out <OutputBamFile> [--minQual <minPhred>] [--log <logFile>] [--oneChrom] [--rmDups] [--force] [--verbose] [--noeof] [--params] [--recab] --refFile <ReferenceFile> [--dbsnp <dbsnpFile>] [--blended <weight>]  

  ./bam dedup --in <InputBamFile> --out <OutputBamFile> [--minQual <minPhred>] [--log <logFile>] [--oneChrom] [--rmDups] [--force] [--verbose] [--noeof] [--params] [--recab]  

 

Additional Recalibration Usage is documented at [[BamUtil: recab#Usage|BamUtil: recab -> Usage]]

= Parameters =

= Parameters =

--params        : print the parameter settings

--params        : print the parameter settings

--recab        : Recalibrate in addition to deduping

--recab        : Recalibrate in addition to deduping

Recab Specific Required Parameters

Additional Recalibration Parameters are documented at [[BamUtil: recab#Parameters|BamUtil: recab -> Parameters]]

--refFile <reference file>    : reference file name

Recab Specific Optional Parameters :  

--dbsnp <known variance file> : dbsnp file of positions

</pre>

{{inBAMInputFile}}

{{inBAMInputFile}}