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Filters BAM/SAM files using SAMTools view.

Element type: filter-bam


ParameterDescriptionDefault valueParameter in Workflow FileType
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 out-formatstring
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.0mapqnumeric
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.