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[[Category:libbam]]
[[Category:BamUtil|filter]]
[[Category:BAM Software]]
[[Category:Software]]
== filter ==
= Overview of the <code>filter</code> function of <code>bamUtil</code> =
The <code>filter</code> option on the [[bamUtil]] executable writes the alignments, filtering them by clipping ends with too high of a mismatch percentage and by marking reads unmapped if the quality of mismatches is too high.
The <code>filter</code> option on the [[Bam|bam executable]] writes the alignments filtering them by clipping ends with too high of a mismatch percentage and by marking reads unmapped if the quality of mismatches is too high.
The following modifications may occur in an alignment:
The following modifications may occur in an alignment:
* FLAG updated to reflect a read is unmapped if it is below the quality of mismatches is too high, or clipping would cause an entire read to be clipped.
* FLAG updated to reflect a read is unmapped if it is below the quality of mismatches is too high, or clipping would cause an entire read to be clipped.
The POS and FLAG fields of an alignment are reflected in the mate's alignment. Thus, the mate also needs to be updated.
The POS and FLAG fields of an alignment are reflected in the mate's alignment. Thus, when the mate also needs to be updated.
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 resort the file.'''
== Fixing the mate/resorting ==
In order to update the mate, samtools fixmate must be run.
In order to update the mate, samtools fixmate must be run.
* samtools sort cannot write to pipes.
* samtools sort cannot write to pipes.
Steps:
===Steps===
# Run this program and pipe it into samtools sort by query name
# Run this program and pipe it into samtools sort by query name
#* <pre>./bam filter --in <your InputFile> --refFile <your reference file> --out -.bam <any other options> | samtools sort -n - tempQuerySort</pre>
#* <pre>./bam filter --in <your InputFile> --refFile <your reference file> --out -.bam <any other options> | samtools sort -n - tempQuerySort</pre>
#* <pre> samtools fixmate tempQuerySort.bam - | samtools sort - finalResult</pre>
#* <pre> samtools fixmate tempQuerySort.bam - | samtools sort - finalResult</pre>
===Example===
~/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
= Parameters =
<pre>
<pre>
Required Parameters:
Required Parameters:
</pre>
</pre>
= Usage =
./bam filter --in <inputFilename> --refFile <referenceFilename> --out <outputFilename> [--noeof] [--qualityThreshold <qualThresh>] [--defaultQualityInt <defaultQual>] [--mismatchThreshold <mismatchThresh>] [--params]
./bam filter --in <inputFilename> --refFile <referenceFilename> --out <outputFilename> [--noeof] [--qualityThreshold <qualThresh>] [--defaultQualityInt <defaultQual>] [--mismatchThreshold <mismatchThresh>] [--params]
= Return Value =
* 0: all records are successfully read and written.
* 0: all records are successfully read and written.
* non-0: at least one record was not successfully read or written.
* non-0: at least one record was not successfully read or written.
= Example Output =
<pre>
<pre>
= FAQ =
This section contains information about what the filters mean, how they work, etc.
This section contains information about what the filters mean, how they work, etc.
:This is requires a bit more logic...and thus gets its own section: [[Bam Executable: Filter#Mismatch Threshold|Mismatch Threshold]].
:This is requires a bit more logic...and thus gets its own section: [[Bam Executable: Filter#Mismatch Threshold|Mismatch Threshold]].
= Mismatch Threshold =
Mismatch threshold is:
Mismatch threshold is:
