...
Parameters
| Parameter | Description | Default value | Parameter in Workflow File | Type | ||||
|---|---|---|---|---|---|---|---|---|
| Output directoryfolder | Select 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-mode | numeric | Custom directory | Custom output directory. | custom-dir | string | |
| Output name | A 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-name | string | |||||
| Output format | Format of an output assembly file. | bam | outout-format | string | ||||
| Region | Regions 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). | region | string | |||||
| MAPQ threshold | Minimum MAPQ quality score. | 0 | mapq | numeric | ||||
| 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-flag | string | |||||
| Skip flag | Skip 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. | flag | string |
...