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BamUtil

351 bytes added, 17:35, 31 August 2011
stats
Uses bamIndex.
--minMapQual : The minimum mapping quality for filtering reads in the baseQC stats.
--dbsnp : The dbSnp file of positions to exclude from baseQC analysis.
--noeof : Do not expect an EOF block on a bam file.
--params : Print the parameter settings
The optional parameters are also used for all types of statistics.
 
Usage:
<pre>
./bam stats --in <inputFile> [--basic] [--qual] [--phred] [--baseQC <outputFileName>] [--maxNumReads <maxNum>] [--unmapped] [--bamIndex <bamIndexFile>] [--regionList <regFileName>] [--minMapQual <minMapQ>] [--dbsnp <dbsnpFile>] [--noeof] [--params]
</pre>
 

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