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BamUtil: filter

1,014 bytes added, 09:29, 6 January 2014
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Also, if the file was sorted, and a POS was changed, the file may no longer be sorted.
'''NOTE: This program does NOT update the mate or resort re-sort the file.'''
== Fixing the mate/resorting ==
~/pipeFilter/bam/bam filter --in ../../originalBamFile.bam --refFile ~/data/human.g1k.v37.fa --out -.bam | samtools sort -n - tempQuerySort; samtools fixmate tempQuerySort.bam - | samtools sort - newResult
 
= Usage =
 
./bam filter --in <inputFilename> --refFile <referenceFilename> --out <outputFilename> [--noeof] [--qualityThreshold <qualThresh>] [--defaultQualityInt <defaultQual>] [--mismatchThreshold <mismatchThresh>] [--params]
= Parameters =
--defaultQualityInt : quality value to use for mismatches that do not have a quality
(Defaults to 20)
--mismatchThreshold : decimal value indicating the maximum ration ratio of mismatches to
matches and mismatches allowed before clipping from the ends
(Defaults to .10)
</pre>
= Usage =Required Parameters=={{InBAMInputFile}}{{refFile}}{{OutBAMOutputFile}} == Optional Parameters =={{noeofBGZFParameter}}=== Quality Threshold (<code>--qualityThreshold</code>) ===In <code>filter</code>, when the sum of the mismatching base qualities is higher than the <code>--qualityThreshold</code>, the read is marked as unmapped. The default threshold is 60. === Default Quality (<code>--defaultQualityInt</code>) ===<code>filter</code> filters reads based on the sum of the base qualities of mismatches. Some reads, however, do not have base qualities. Use <code>--defaultQualityInt</code> to specify the base qualities to use for mismatches that do not have quality values. The default is 20. === Mismatch Threshold (<code>--mismatchThreshold</code>) ===<code>filter</code> clips the ends of reads if the ratio of mismatches to matches and mismatches is higher than the decimal parameter, <code>--mismatchThreshold</code>. The default is .10. {{paramsParameter}} {{PhoneHomeParameters}}
./bam filter --in <inputFilename> --refFile <referenceFilename> --out <outputFilename> [--noeof] [--qualityThreshold <qualThresh>] [--defaultQualityInt <defaultQual>] [--mismatchThreshold <mismatchThresh>] [--params]
= Return Value =

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