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, 13:01, 13 October 2010
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| === Parameters === | | === Parameters === |
| <pre> | | <pre> |
− | Required Parameters:
| + | Required Parameters: |
− | --in : the SAM/BAM file to be read
| + | --in : the SAM/BAM file to be read |
− | --refFile : the reference file
| + | --refFile : the reference file |
− | --out : the SAM/BAM file to write to
| + | --out : the SAM/BAM file to write to |
− | Optional Parameters:
| + | Optional Parameters: |
− | --noeof : do not expect an EOF block on a bam file.
| + | --noeof : do not expect an EOF block on a bam file. |
− | --qualityThreshold : maximum sum of the mismatch qualities before marking
| + | --qualityThreshold : maximum sum of the mismatch qualities before marking |
− | a read unmapped. (Defaults to 60)
| + | a read unmapped. (Defaults to 60) |
− | --defaultQualityInt : quality value to use for mismatches that do not have a quality
| + | --defaultQualityInt : quality value to use for mismatches that do not have a quality |
− | (Defaults to 20)
| + | (Defaults to 20) |
− | --mismatchThreshold : decimal value indicating the maximum ration of mismatches to
| + | --mismatchThreshold : decimal value indicating the maximum ration of mismatches to |
− | matches and mismatches allowed before clipping from the ends
| + | matches and mismatches allowed before clipping from the ends |
− | (Defaults to .10)
| + | (Defaults to .10) |
− | | + | --params : print the parameter settings |
| </pre> | | </pre> |
| | | |
| === Usage === | | === Usage === |
| | | |
− | ./bam filter --in <inputFilename> --refFile <referenceFilename> --out <outputFilename> [--noeof] [--qualityThreshold <qualThresh>] [--defaultQualityInt <defaultQual>] [--mismatchThreshold <mismatchThresh>] | + | ./bam filter --in <inputFilename> --refFile <referenceFilename> --out <outputFilename> [--noeof] [--qualityThreshold <qualThresh>] [--defaultQualityInt <defaultQual>] [--mismatchThreshold <mismatchThresh>] [--params] |
| | | |
| === Return Value === | | === Return Value === |
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| === Example Output === | | === Example Output === |
| <pre> | | <pre> |
− | 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. | | open and prefetch reference genome /home/mktrost/data/human.g1k.v37.fa: done. |