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BamUtil: filter

637 bytes added, 14:55, 30 September 2010
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=== Parameters ===
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Required Parameters: --in : the SAM/BAM file to be read --refFile : the reference file --out : the SAM/BAM file to write to Optional Parameters: --noeof : do not expect an EOF block on a bam file. --qualityThreshold : maximum sum of the mismatch qualities before marking a read unmapped. (Defaults to 60) --defaultQualityInt : quality value to use for mismatches that do not have a quality (Defaults to 20) --mismatchThreshold : decimal value indicating the maximum ration of mismatches to matches and mismatches allowed before clipping from the ends (Defaults to .10) 
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=== Usage ===
./bam filter --in <inputFilename> --refFile <referenceFilename> --out <outputFilename> [--noeof] [--qualityThreshold <qualThresh>] [--defaultQualityInt <defaultQual>] [--mismatchThreshold <mismatchThresh>]
=== Return Value ===

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