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Parameters

ParameterDescriptionDefault valueParameter in Workflow FileType
Output directoryfolderSelect 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.
out-modenumericCustom directoryCustom output directory.custom-dirstring
Output nameA name of an output BAM/SAM file. If the default of empty value is provided the output name is the name of the first BAM/SAM file with .filtered extentionextension.
 outout-namestring
Output formatFormat of an output assembly file.bam outout-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 output regions of chr2 between 1000 and 2000 including the end pointendpoint. To input, multiple regions use the space seprator separator (e.g. chr1 chr2 chr3:1000-2000).
regionstring
MAPQ thresholdMinimum MAPQ quality score.0mapqnumeric
Accept flag

Only output alignments with the selected items. Select the items in the combo box to configure the bit flag. Do not select the items to avoid filtration by this parameter.


accept-flagstring
Skip flagSkip alignment with the selected items. Select the items in the combobox combo box to configure the bit flag. Do not select the items to avoid filtration by this parameter.
flagstring


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