Filters BAM/SAM files using SAMTools view.
Parameters in GUI
| Parameter | Description | Default value |
|---|---|---|
| Output directory | 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. | |
| Custom directory | Custom output directory. | |
| Output name | A 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 format | Format of an output assembly file. | bam |
| 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 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 threshold | Minimum MAPQ quality score. | 0 |
| Skip flag | Skip 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
| Parameter | Parameter in the GUI | Type |
|---|---|---|
| out-mode | Output directory | numeric |
| custom-dir | Custom directory | string |
| out-name | Output name | string |
| out-format | Output format | string |
| region | Region | string |
| mapq | MAPQ threshold | numeric |
| flag | Skip flag | string |
Input/Output Ports
The element has 1 input port:
Name in GUI: BAM/SAM File
Name in Workflow File: in-file
Slots:
| Slot In GUI | Slot in Workflow File | Type |
|---|---|---|
| Source URL | input-url | string |
And 1 output port:
Name in GUI: Filtered BAM/SAM files
Name in Workflow File: out-file
Slots:
| Slot In GUI | Slot in Workflow File | Type |
|---|---|---|
| Source URL | output-url | string |