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  • Filter BAM/SAM Files Element
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Filters BAM/SAM files using SAMTools view.

Parameters in GUI

ParameterDescriptionDefault value
Output directorySelect an output directory. Custom - specify the output directory in the 'Custom directory' parameter. Workflow - internal workflow directory. Input file - the directory of the input file. 
Custom directoryCustom output directory. 
Output nameA name of an output BAM/SAM file. If default of empty value is provided the output name is the name of the first BAM/SAM file with .filtered extention. 
Output formatFormat of an output assembly file.bam
RegionRegions to filter. For BAM output only. chr2 to output the whole chr2. chr2:1000 to output regions of chr 2 starting from 1000. chr2:1000-2000 to ouput regions of chr2 between 1000 and 2000 including the end point. To input multiple regions use the space seprator (e.g. chr1 chr2 chr3:1000-2000). 
MAPQ thresholdMinimum MAPQ quality score.0
Skip flagSkip alignment with the selected items. Select the items in the combobox to configure bit flag. Do not select the items to avoid filtration by this parameter. 

Parameters in Workflow File

Type: filter-bam

ParameterParameter in the GUIType
out-modeOutput directorynumeric
custom-dirCustom directory


 out-nameOutput namestring
 out-formatOutput formatstring
 mapqMAPQ thresholdnumeric
 flagSkip flagstring

Input/Output Ports

The element has 1 input port:

Name in GUI: BAM/SAM File

Name in Workflow File: in-file


Slot In GUISlot in Workflow FileType
Source URLinput-urlstring

And 1 output port:

Name in GUI: Filtered BAM/SAM files

Name in Workflow File: out-file


Slot In GUISlot in Workflow FileType
Source URLoutput-urlstring
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