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351 bytes added
, 18:35, 31 August 2011
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| Uses bamIndex. | | Uses bamIndex. |
| --minMapQual : The minimum mapping quality for filtering reads in the baseQC stats. | | --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. | | --noeof : Do not expect an EOF block on a bam file. |
| --params : Print the parameter settings | | --params : Print the parameter settings |
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| The optional parameters are also used for all types of statistics. | | The optional parameters are also used for all types of statistics. |
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| + | 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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