3,045
edits
Changes
From Genome Analysis Wiki
Jump to navigationJump to searchno edit summary
Also, if the file was sorted, and a POS was changed, the file may no longer be sorted.
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 the file.'''
'''NOTE: This program does NOT update the mate or re-sort the file.'''
== Fixing the mate/resorting ==
== 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
~/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 =
= Parameters =
--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 ratio 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)
</pre>
</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}}
= Return Value =
= Return Value =
