Changes

= Usage =

= Usage =

  ./bam dedup (options) --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] --refFile <ReferenceFile> [--dbsnp <dbsnpFile>] [--blended <weight>]  

= Parameters =

= Parameters =

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<pre>

equired parameters :

Required parameters :

--in <infile>  : input BAM file name (must be sorted)

--in <infile>  : input BAM file name (must be sorted)

--out <outfile> : output BAM file name (same order with original file)

--out <outfile> : output BAM file name (same order with original file)