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BamUtil: filter

136 bytes removed, 12:01, 13 October 2010
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=== Parameters ===
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) --params : print the parameter settings
=== Usage ===
./bam filter --in <inputFilename> --refFile <referenceFilename> --out <outputFilename> [--noeof] [--qualityThreshold <qualThresh>] [--defaultQualityInt <defaultQual>] [--mismatchThreshold <mismatchThresh>] [--params]
=== Return Value ===
=== Example Output ===
The following parameters are available. Ones with "[]" are in effect:
Input Parameters
--in [../../originalBamFile.bam],
--out [-.bam], --refFile [/home/mktrost/data/human.g1k.v37.fa], --noeof,
--qualityThreshold [60], --defaultQualityInt [20], --mismatchThreshold [0.10]
open and prefetch reference genome /home/mktrost/data/human.g1k.v37.fa: done.

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